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1-D water column framework with implicit horizontal fluxes due to vertical divergence in the flow (zero horizontal gradients assumed); parameterization of explicit horizontal flux divergence effects by mean and/or autoregressive random perturbations for individual tracers; support for dependency of perturbations on local tracer concentrations (using tracer transformations); options for relaxation towards reference fields and/or direct replacement of individual tracers by prescribed external data
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Photosynthesis light limitation options: light attenuation coeff. from Anderson spectral model approximation with depth & pigment dependency (Anderson, T.R.,1993, Limnol. Oceanogr. 38, 1403-1419) or simple linear pigment dependency, optional noon path-length adjustment; chlorophyll-specific absorption from Anderson 1993 spectral model approximation or constant; photosynthetic response from Evans and Parslow daily mean model (Evans, G.T. & Parslow, J.S., 1985, Biol. Oceanogr. 3, 327-347) or Platt et al. daily mean model (Platt, T., Sathyendranath, S. & Ravindran, P., 1990, R. Soc. Lond. Ser. B 241, 101-111) or point-in-time photosynthesis model for resolving diel cycle
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Generic ecosystem model code interface supporting multiple plankton types
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Support for sequential chlorophyll data assimilation (Hemmings, J.C.P, Barciela, R.M. & Bell, J.M., 2008, J. Mar. Res. 66, 87-126)
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Simulation input tables (Each item is optional by default - MarMOT provides default values for missing data where appropriate and checks that configuration-specific data requirements are met)
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Model parameter set items - one table for each ecosystem model
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Data assimilation parameter set items - one table for each ecosystem model with chlorophyll data assimilation
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Option parameter set item: ecosystem model selection (initialized variables are treated as passive tracers if no model), photosynthesis options & controls, advection scheme selection, diffusion and mixing controls, perturbation options & controls, tracer relaxation controls, time-stepping parameters, temporal interpolation modes for forcing data, default tracer relaxation rates & initial conditions
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Time axis parameter set item: base year, periodic forcing switch for annual forcing, year length
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Time period parameter set item: simulation start and finish times
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Environment parameter set item: maximum depth, latitude, default values for forcing variables below
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Perturbation seed parameter set item: seed values for autoregressive random perturbations
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Misfit control parameter set item: variable-specific log or sqrt transformations for model-data misfit calculation
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Vertical grid item (on level grid): depths for up to 500 levels
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Initial profile item (defined on level grid): initial profiles of primary tracers and/or composition ratios for deriving secondary tracers (default to values in option parameter set item)
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Scalar forcing item/items (defined on an arbitrary time grid): solar irradiance, mixed layer depth, surface salinity, atmospheric pCO2, dust deposition, chlorophyll observations for data assimilation, depth-invariant full-depth forcing variables (default to constant forcing from environment parameter set item or option item); option for dividing variables between multiple items on different time grids
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Full depth profile forcing item/items (defined on level and arbitrary time grid): vertical diffusion coefficient, vertical velocity, temperature, means and standard deviations for tracer perturbations, relaxation rates and reference profiles for tracer relaxation (default to depth-invariant forcing from scalar forcing item); option for dividing variables between multiple items on different time grids
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Observation set item (defined at arbitrary times and depths): 'observed' values of any output variable, observation weights; can use previous output as synthetic observations
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Simulation output tables (Data are selectable for output at table or variable level)
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Options table: options applicable to simulation including active defaults
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Surface and scalar variables tables (end of time step, daily mean, monthly mean & annual mean versions): top-level values of full-depth variables below plus surface forcing and scalar diagnostics
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Full-depth profile tables (end of time step, daily mean, monthly mean & annual mean versions): full-depth forcing, primary tracers, composition ratios, derived tracers and full-depth diagnostics
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Surface and scalar data assimilation variables table (output at analysis times): surface/scalar data assimilation diagnostics
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Full-depth data assimilation profiles table (output at analysis times): full-depth data assimilation diagnostics
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Misfit table: simulated and observed values, model-data differences, weights and weighted misfits (squared differences) at each observation point
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Cost table: mean weighted misfit over all observations
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Output cost function value given by mean weighted misfit over all observations for all specified simulation cases
