Up Close and Personal with ECO Lab
•
3 likes•1,053 views
2015 DHI UK & Ireland Symposium Training seminars Wednesday 22 April 2015 ECO Lab – Up Close and Personal General introduction to ECO Lab - DHI’s environmental modelling system (Michael Potthoff, DHI Denmark)
Recommended
Recommended
More Related Content
What's hot
What's hot (20)
Viewers also liked
Viewers also liked (20)
Similar to Up Close and Personal with ECO Lab
Similar to Up Close and Personal with ECO Lab (20)
More from Stephen Flood
More from Stephen Flood (20)
Recently uploaded
Recently uploaded (20)
Up Close and Personal with ECO Lab
- 1. ECO Lab – Up Close and Personal 2015 DHI UK & IRELAND Symposium Michael Potthoff, DHI Denmark General introduction to ECO Lab - DHI’s environmental modelling system © DHI
- 2. Why we need Ecological Models? • Intelligent interpolation, extrapolation • Budgeting tool • Quantification/qualification • Management tool • Hypothesis testing • EIA © DHI
- 3. What kind of models are used (for ecological modelling)? In Ecology a large range of different model(-types) are used: • Process/ Biogeochemical models • Individual / Agent based models • Statistical models • Population models • Conceptual models • … © DHI
- 4. Process orientated Modelling / bio-geochemical Models Definition: “Models describing the fate of masses / concentrations due to associated processes” © DHI 𝐶6 𝐻12 𝑂6 + 6 𝑂2 ℎ𝑣 6 𝐶𝑂2 + 6 𝐻2 𝑂 𝑑 𝑉𝐴𝑅𝐼𝐴𝐵𝐿𝐸 𝑑𝑡 = + 𝑝𝑟𝑜𝑐𝑒𝑠𝑠1 − 𝑝𝑟𝑜𝑐𝑒𝑠𝑠2 … Differential equations:
- 5. Agent Based Modelling Definition: “Models describing the autonomic behavior and states of agents, objects or individuals” © DHI
- 6. Stochastic Models Definition: “Regression Models” © DHI 𝑓 𝑥 = 𝛼𝐺 𝑥 + 𝐻(𝐽 𝑥 )
- 7. Population Models Definition: − “Describe the state of a population” − Typically matrix-models © DHI
- 8. What is this „ECO Lab“? • A numerical laboratory for ecological modelling in aquatic environments − Open Equation solver (for coupled ordinary differential equations) − Designed for descriptions of processes of chemistry, ecology etc. − All equations, parameters contained in generic, portable ECO Lab templates • Seamless coupled into most Mike-by-DHI hydrodynamic engines − Transport calculations, result representation etc. © DHI
- 9. © DHI 𝐶6 𝐻12 𝑂6 + 6 𝑂2 ℎ𝑣 6 𝐶𝑂2 + 6 𝐻2 𝑂 The “system” ECO Lab provides an infrastructure to implement process orientated and agent based (ABM) models • Abstraction of different data items − (State-) Variables, parameter- and input data, calculations • A expression language − similar to expression written in an spreadsheet calculator (not macros/VB!) What is this „ECO Lab“?
- 10. What is this „ECO Lab“? • The Model formulation module − Template Editor • The Application Module − Using a model template in a specific hydrodynamic environment ECO Lab is essentially split into two parts © DHI
- 11. Typical applications • Rivers and wetlands − Oxygen, transport/decay of pollutants − Retention of nutrients • Lakes and reservoirs − Eutrophication − Cyanobacteria • Estuaries − Eutrophication − Macrphytes − Metals • Coastal waters and seas − Eutrophication − Bathing water quality − Aquaculture © DHI
- 12. Functional dependency of ECO Lab © DHI Hydraulic modelling Water level, Flux, discharge Transport (advection-dispersion) Initial values, sources, boundaries ECOLab Process descriptions Parameter,… Water quality information MIKE HD-Engine
- 13. ECO Lab - Workflow Project Analysis Data Collection Template? Hypothesis/ theory Ecological Model development Setup & run model Results OK? Theory OK? Calibration Solution ECO Lab Templates © DHI
- 14. Available templates • A number of template families come with ECO Lab • Various complexity inside the families • Use “out-of-the-box” or as starting point for own development © DHI
- 15. Available templates • Generic − Enterococci_Ecoli.ecolab − EutrophicationModel1.ecolab − EutrophicationModel13AlgaeSediment.ecolab − EutrophicationModel1SedimentBenthic Vegetation.ecolab − EutrophicationModel1TropicalMangroves.ecola b − EutrophicationModel2.ecolab − HeavyMetals.ecolab − Xenobiotics.ecolab • M11 − WQlevel1.ecolab − WQlevel1Coli.ecolab − WQlevel2.ecolab − WQlevel3.ecolab − WQlevel4.ecolab − WQlevel4Coli.ecolab − WQlevel4ColiPhos.ecolab − WQlevel5.ecolab − WQlevel6.ecolab − WQlevel6Coli.ecolab − WQlevel6ColiPhos.ecolab • M21/M3 − WQnutrients.ecolab − WQnutrientsChl.ecolab − WQsimple.ecolab − WQsimpleColi.ecolab − WQsimpleTandS.ecolab − WQsimpleTandSCOLI.ecolab © DHI
- 16. Water Quality Templates - WQ • The WQ templates describe oxygen conditions and degradation of organic matter, resulting excess levels of nutrients and the survival of bacteria, in water bodies. • Templates cover simple combinations of variables such as BOD-DO and more complex combinations, including the most significant inorganic forms of nitrogen and phosphorus. http://www.dhisoftware.com/ECOLab/Description/ECOLabTemplates_WQ.htm © DHI
- 17. EutrophicationTemplates - EU • The EU Templates describes nutrient cycling, phytoplankton and zooplankton growth, growth and distribution of rooted vegetation and macro algae in addition to simulating oxygen conditions. http://www.dhisoftware.com/ECOLab/Description/ECOLabTemplates_EU.htm EU details © DHI
- 18. Heavy Metal / Xenobiotics Templates – ME / XE • The ME/XE Templates describes the adsorption/desorption of metals/xenobiotics to suspended matter, the sedimentation of sorbed matter to the seabed as well as resuspension of settled material. • It also includes the exchange between the particulates of the seabed sediment and interstitial waters of the bed http://www.dhisoftware.com/ECOLab/Description/ECOLabTemplates_EU.htm © DHI
- 19. Coli Bacteria Template - Coli • This template describes the spreading and the decay of coliform bacteria. The decay is described as dependent of light, salinity and temperature. • The template is usually applied in environmental management of areas used for recreation and bathing to describe bathing water quality. http://www.dhisoftware.com/ECOLab/Description/ECOLabTemplates_Coli.htm © DHI
- 20. General introduction to ECOLab ECOLab internals The Model formulation module Template Editor © DHI
- 21. Functional dependency of ECO Lab Hydraulic modelling Water level, Flux, discharge Transport (advection-dispersion) Initial values, sources, boundaries ECOLab Process descriptions Parameter,… Water quality information © DHI
- 22. ECO Lab Items / Navigation Details of selected item Status / Error Messages Model formulation module / template editor © DHI
- 23. • ECOLab template: • All process descriptions, variable definitions etc. (the “model”) are stored in a separate file. • This “template” can be linked into a hydrodynamic engine (The Application Module) • The same ECO Lab template can be used in 1D, 2D or 3D HD models! • Parameterisation of a model/template is done in the setup Model formulation module / template editor © DHI
- 24. © DHI Model formulation module / template editor
- 25. ECOLab elements • State Variables − The information of “interest”, i.e. biomass, concentration • Constants − (time invariant) parameter, e.g. rates, stoichiometric relationships • Forcing − (external) Factors influencing the calculations, e.g. temperature, flow • Auxiliary Variables − Intermediate calculations, outputs • Process − Describing the change rate of state variables • Derived outputs − Pure output items (based on the data values at the end of a time step) © DHI
- 26. State Variables • Describe the variables “of interest”, i.e. mass, concentration • Can be transported or stationary (i.e. benthic biomass) • Expression: right-hand side of the ODE © DHI 𝑑[𝑉𝐴𝑅𝐼𝐴𝐵𝐿𝐸 𝐴] 𝑑𝑡 = −𝒅𝒆𝒂𝒄𝒚 + ⋯ In the expression only reference to Process are allowed! State variables represent the only “preserved” information in time
- 27. Constants • Describe temporal invariant factors • Usually (growth) rates, stoichiometric relations, habitat type etc. • May vary spatial • Some “built-in” constants, e.g. timestep length © DHI 𝑡ℎ𝑒𝑡𝑎 = 1.07
- 28. Forcing • Both potential temporal and spatial varying external factors • Typical examples: temperature, density, flow information, sun radiation, wind speed etc. • A number of “built-in” forcing exist, allowing to query HD-engine information − Only if provided by the engine, otherwise user specified! © DHI 𝑡𝑒𝑚𝑝 = [𝑏𝑢𝑖𝑙𝑡 − 𝑖𝑛 𝑡𝑒𝑚𝑝𝑒𝑟𝑎𝑡𝑢𝑟𝑒]
- 29. Built-in forcings © DHI HD calculations: Water Layer Height Water Surface Level Water Depth Horizontal Current Speed Horizontal Current Direction Vertical Current Speed Water Surface Slope in Flow Direction Salinity Temperature Water Density HD forcings: Wind Velocity Wind Direction From HD set-up Bed Area of Grid Cell Flooded Area of Grid Cell Surface Area of Grid Cell Volume of Grid Cell Horizontal Grid Cell Flux Vertical Grid Cell Flux From HD simulation and set-up files
- 30. Auxiliary Variables • Intermediate calculations (user function) • Additional outputs © DHI 𝑡𝑒𝑚𝑝 𝑐𝑜𝑟𝑟𝑒𝑐𝑡𝑖𝑜𝑛 = 𝑘 ∗ 𝑝𝑜𝑤(𝑡ℎ𝑒𝑡𝑎, 𝑡𝑒𝑚𝑝 − 20)
- 31. Process • Describe the change of a state variable • Expression can refer to any other item (besides derived outputs) © DHI decay = 𝐴 ∗ 𝑡𝑒𝑚𝑝 𝑐𝑜𝑟𝑟𝑒𝑐𝑡𝑖𝑜𝑛
- 32. Derived Outputs • “pure” output information • Can summarise e.g. water column information © DHI
- 33. ECOLab expressions • ECOLab uses an expression language similar to a spreadsheet calculator • Std. mathematical expressions • Built-in functions • User variables • IF-THEN-ELSE constructs (nested) Variable = A * sin(0.5) / ( 1+ XY) Variable(name) and assignment are implicitly! Equation has to be specified by the user! © DHI
- 34. ECOLab expressions • ECOLab uses an expression language similar to a spreadsheet calculator • Std. mathematical expressions • Built-in functions • User variables • IF-THEN-ELSE constructs (nested) Variable = A * sin(0.5) / ( 1+ XY) © DHI
- 35. Math functions ABS(X) ARCCOS(X) ARCSIN(X) ARCTAN(X) ARCTAN2(X,Y) COS(X) COSH(X) EXP(X) LN(X) LOG(X) MAX(X,Y) MIN(X,Y) POW(X,Y) SIN(X) SINH(X) SQR(X) SQRT(X) TAN(X) TANH(X) PI() … and more, e.g. biological functions IF (conditional expression) THEN (expression) ELSE (expression) IF(conditional expression, expression if true, expression if false) Logical functions © DHI
- 36. Work with the template editor Start Template Editor Scope Spatial variation Process type Explain © DHI
- 37. Calculation order • ECOLab calculations are strongly sequential • You can just refer to “known” data, i.e. something that has been computed • Similar to a spread-sheet calculation − For each layer Read initial State variable concentrations Read Constant values Read Forcing values Calculate Auxiliary variables Calculate Process variables Numeric integration of state variables Calculation of Derived Outputs © DHI
- 38. 1.) Loading state variables 2.) Loading constants 3.) Loading forcing 4.) Calculate auxiliary expressions 5.) Calculate process expressions 6.) Integration 7.) Calculate derived outputs 𝑑𝑒𝑐𝑎𝑦 = 𝑟 ∗ 𝑓𝑡𝑒𝑚𝑝 ∗ 𝐴 𝐴 = 1.25 𝑟 = 0.6931 𝑓𝑡𝑒𝑚𝑝 = 𝜃 𝑇𝑒𝑚𝑝−20.0 𝑇𝑒𝑚𝑝 = 15.0 𝑑𝐴 𝑑𝑡 = −𝑑𝑒𝑐𝑎𝑦 + ⋯ D𝑒𝑟𝑖𝑣𝑒𝑑 𝑜𝑢𝑡𝑝𝑢𝑡1 = 𝐴 + ⋯ 𝜃 = 1.072 At+dt= At+dt*(-decay + … ) (numeric integration e.g. Euler scheme) © DHI
- 39. Building A simple BOD-DO model Model formulation We will build a simple BOD-DO (dissolved oxygen) model with two state variables, dissolved oxygen (DO) and BOD (org. carbon pollutant). Oxygen is coupled to the atmosphere by a reaeration process. We do not include the atmosphere or CO2 as individual variables in our model. BOD is organic carbon and expressed as amount of oxygen needed to respire a certain amount of it. © DHI
- 40. A simple BOD-DO model We can set up the following equations to build an ECO Lab model: 𝑑𝐷𝑂 𝑑𝑡 = 𝑟𝑒𝑎𝑒𝑟𝑎𝑡𝑖𝑜𝑛 − 𝐵𝑂𝐷 𝑑𝑒𝑐𝑎𝑦 𝑑𝐵𝑂𝐷 𝑑𝑡 = −𝐵𝑂𝐷 𝑑𝑒𝑐𝑎𝑦 The BOD decay is a simple 1st order process: 𝐵𝑂𝐷 𝑑𝑒𝑐𝑎𝑦 = 𝑟 ∗ 𝐵𝑂𝐷 With r = BOD decay rate © DHI
- 41. A simple BOD-DO model The reaeration is driven by the gradient between the oxygen saturation concentration and the current oxygen concentrations. It can also be seen as a simple process: 𝑟𝑒𝑎𝑒𝑟𝑎𝑡𝑖𝑜𝑛 = 𝑘 ∗ (𝐷𝑂𝑠𝑎𝑡𝑢𝑟𝑎𝑡𝑖𝑜𝑛 − 𝐷𝑂) with k = reaeration rate DOsaturation = max oxygen saturation concentration, depends on temperature and salinity Water body Atmosphere O2 Reaeration © DHI
- 42. Building it in ECOLab Equations: 𝑑𝐷𝑂 𝑑𝑡 = 𝑟𝑒𝑎𝑒𝑟𝑎𝑡𝑖𝑜𝑛 − 𝐵𝑂𝐷 𝑑𝑒𝑐𝑎𝑦 𝑑𝐵𝑂𝐷 𝑑𝑡 = −𝐵𝑂𝐷 𝑑𝑒𝑐𝑎𝑦 𝐵𝑂𝐷 𝑑𝑒𝑐𝑎𝑦 = 𝑟 ∗ 𝐵𝑂𝐷 𝑟𝑒𝑎𝑒𝑟𝑎𝑡𝑖𝑜𝑛 = 𝑘 ∗ (𝐷𝑂𝑠𝑎𝑡𝑢𝑟𝑎𝑡𝑖𝑜𝑛 − 𝐷𝑂)Start Template Editor View video… © DHI
- 43. General introduction to ECOLab Using ECOLab templates The Application Module Interfacing with hydrodynamic engines © DHI
- 44. Interfacing with hydrodynamic engines • ECO Lab templates represent the model − Variable definitions − Parameter definitions − Equations • The hydrodynamic engine provides the „environment“ − Water flow − Transport − Built-in parameter values − Output writing © DHI
- 45. Interfacing with hydrodynamic engines • Hydrodynamic setup − ECO Lab seamless integrated into the engine setup − Parameterization of the ECO Lab template • Initial values • Dispersion settings • Parameter values (constants/ forcing) • Output specifications • Solution methods − “Common” look&feel in all HD engines (but M11 ) − If a template is structurally changed it must be reloaded! © DHI
- 46. Running Mike…. © DHI Mike11 Mike21 Mike3 Mike21 FM Mike3 FM Using the template with…
- 47. ABM using ECO Lab Agent Based Modelling / Individual Based Modelling © DHI
- 48. Agent Based Modelling Definition: “Models describing the autonomic behavior and states of agents, objects or individuals” © DHI
- 49. Agent Based Modelling Example: Simple ABM, locate and feeding on a resource Click to play video © DHI
- 50. Agent Based Modelling Example: Coral larvae © DHI
- 51. Agent Based Modelling Example: Coral larvae, spawning, dispersion and settling Click to play video © DHI
- 52. Agent Based Modelling using ECO Lab • Supported by the FM-HD engines (MIKE21FM, MIKE3FM) • Based on a combination of ECO Lab and particle tracking © DHI
- 53. Agent Based Modelling using ECO Lab • Supported by the FM-HD engines • Based on a combination of ECO Lab and particle tracking © DHI Standard particle tracking: pure passive movement in the flow field
- 54. Agent Based Modelling using ECO Lab • Supported by the FM-HD engines • Based on a combination of ECO Lab and particle tracking © DHI Where do I want to go ? ABM simulation: active, directed movement
- 55. Agent Based Modelling using ECO Lab • Supported by the FM-HD engines • Based on a combination of ECO Lab and particle tracking ECO Lab descriptions • State variables • dMass / dt = Growth • Constants • Growthrate = 1.05 • Sensing functions • Arithmetic expressions • Growth = Growthrate * Mass • Movement vectors • Direction =… • Speed = … • Vertical Speed = … © DHI
- 56. Agent Based Modelling using ECO Lab Start ABM Example© DHI
- 57. © DHI • S.E. Jørgensen and G. Bendoricchio Fundamentals of Ecological Modelling 3rd Edition, Elsevier • V.Grimm S.F. Railsback Individual-based Modeling and Ecology Princeton University Press • K.Soetaert, P.M.J. Herman 2009, A Practical Guide to Ecological Modelling Springer 2009 • E.J. Rykiel ,1996 Testing ecological models: the meaning of validation Ecological Modelling 90(1996), 229-244 • Colin Reynolds Ecology of Phytoplankton Cambridge Press • T.E.L. Langford 1990, Ecological Effects of Thermal Discharges Elsevier ISBN 1-85166-451-3 • Rates, Constants, and Kinetics Formulations in Surface Water Quality Modeling (Second Edition) (EPA/600/3-85/040) US-EPA • A. Satelli, K. Chan and E.M. Scott Sensitivity Analysis 2000, Wiley & Sons • Literature / Further readings
- 58. Thank you Michael Potthoff, MPO@dhigroup.com © DHI
- 59. Eutrophication model org. matter, particulate N & P Photosynthesis Reaeration SunlightPollution: BOD, NH3, NH4, NO3, PO4 NO3 -, NH3, NH4 -, PO4 3-, O2 Sedimentation resuspension Diffusion Adsorbtion Diffusion desorbtion phytoplankton Nutrient transformation Filtration
- 60. Detritus N Pollution sources (NO3 -, NO2 -, NH4 +, NH3, Organic-N) Inorg. N Uptake Phytoplankton N Sedimen- tation Sediment Mineralisation Sediment Detritus & Phytoplankton N Sloughing/death Zooplankton N Grazing Death/egestion Sedimen- tation Resus- pension Mineralisation Uptake Benthic vegetation EU – nitrogen cycle
- 61. EU – phosphorous cycle Detritus P Pollution sources (PO4 3-, Organic-P) PO4 Uptake Phytoplankton P Sedimen- tation Sediment Mineralisation Sediment Detritus & Phytoplankton P Sloughing/death Zooplankton P Grazing Death/egestion Sedimen- tation Resus- pension Mineralisation Uptake Benthic vegetation
- 62. EU – phosphorous in the sediment Sedimentation ResuspensionDiffusion Fe3+ Fe2+ PO4 PO4 PO4 PO4 PO4 PO4 PO4 PO4 Oxygendecrease Sediment detritus P Sediment PO4 3- Mineralisation Plant uptake MineralisationPO4 3- Detritus P
- 63. Detritus C Pollution sources (Detritus C) Phytoplankton C Sedimen- tation Sediment Mineralisation Sediment Detritus Sloughing/death Zooplankton C Grazing Death/egestion Sedimen- tation Resus- pension Mineralisation Benthic vegetation EU – carbon cycle CO2 IN IP
- 64. EU – phytoplankton processes Phytoplankton C Phytoplankton N Phytoplankton P Inorganic N Inorganic P zooplankton C zooplankton N Zooplankton P Grazing Mineralisation Detritus N, P, C Death/sloughning Death/egestion
- 65. Back….
- 66. Horizontal space discretisation in ECO Lab • None • Only one value for the whole domain back „Spatial Variation“ • Horizontal (2D) • Can vary in all grid points but the same in all layers of the water column under the grid point • Horizontal and vertical (3D) • Can vary in all grid points and all layers © DHI
- 67. Vertical space discretisation in ECO Lab, “SCOPE” definition Scope Stands for Meaning NOT_SPECIFIED - - WS Water surface Just defined in the surface layer WC Water column Defined in the whole water column WB Water bed Defined as the bed layer between the water column and the sediment SED Sediment only defined in the sediment layer Water body Sediment Atmosphere WS WC WB SED ECOLab Scope (Water Surface) (Water Column) (Water Bed) (Sediment) back © DHI
- 68. Process type Process „transform“ one state variable into another one (flow of matter). They can also be used to move matter between layers in a multi-layered setup (3D setup) Process type • Transformation (standard) , applies to the same layer • Buoyancy, move to the upper layer • Settling, move to the lower layer backDetails © DHI
- 69. “Settling” in the water column • ECOLab can handle settling / buoyancy process in multi-layer models Water body Sediment Atmosphere 𝑑[𝐵] 𝑑𝑡 = … − 𝑝4 B1 B2 B3 B1 = … – p4_1 B2 = … – p4_2 + p4_1 B3 = … – p4_3 + p4_2 layer 1 2 3 back © DHI