Jean-Luc de Kok Flemish Institute for Technological Research (VITO)

Cluster Workshop Amsterdam- KobenhåvnFebruary 17-20, 2009

Science and Policy Integration for COastal System Assessment

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Jean-Luc de Kok

Flemish Institute for Technological Research (VITO)

TOWARDS A GENERIC MODEL LIBRARY



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Outline Introduction: state of affairs

Why a generic model library ?

What is a generic model library ?

Requirements of generic MBBs

SSA Extend models: what do have so far?

Designing the library: steps to take

The Online Data Portal: ready for testing

Data management

Extend-PCraster interface: a quick outlook

Appraisal Step

Discussion



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Introduction



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Situation Feb 2009:

based on SR and review of Extend models :

14 working Extend models covering range of topics

- eutrophication / waterquality (9)

- fisheries / shell species (4)

- hydrology (4)

- tourism (3)

- economics / social dimension (4)

4 sites with custom libraries, 6 use H blocks, 6 do not , 2 use a mix



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Note 1:

Science can (at least for some time) do

without a model library, but a good model

library cannot do without science

That’s why the design of the library is a joint

task for the SSAs and supporting WPs



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Note 2:

Model review is technically oriented, and not

meant to critisize the scientific quality



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Why a generic model library ?



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Several advantages:

easier to build & expand your models

easier to maintain your models

easier to exchange (parts of) models with colleagues

creating next generation models (post Spicosa)

knowledge management in a practical format

iterative model improvement rather than “reinventing the wheel over and over again ...”



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What is a generic model library ?



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Collection of reusable model components:



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SYSTEM

SUB SYSTEM

DISCIPLINARY MODEL

STATE VARIABLE

PROCESS

OPERATORS, MATHEMATICAL FUNCTIONS, PRIMITIVES

systemmodel

environmentalmodel

economicmodel

hydrologic model

ecologic model

state variableNitrogen

state variablePlankton

processdenitrification

processmineralisation

output &indicators

SPICOSAtoolboxLibrary

SPICOSAmodelblocksLibrary

more unique/less generic systems

fishgrowth

returnon

investment

run offmodule

RK4integrate

Areaplotter

1Dadvection

1Ddiffusion

PCRASTERinterface

ExtendSimvalue Library



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What should be in the model and

what not to make it generic ?



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initial velocity Vy

at t = 0

Vx

gravitational accelation

g

initial position at t = 0

(x,y)0

Example: ballistic bullet trajectory

bullet mass

M

position at time t

(x,y)t ?



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Model block BulletTrajectoryOnEarth :

Outside model: mass M

initial position

initial velocity

Inside model: gravitational acceleration

(universal, model-specific constant)



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Model block BulletTrajectoryInUniverse :Outside model: mass M

initial position

initial velocity

gravitational acceleration



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Conclusions:

1. The more specific a model is the more

is inside it

2. More generic models receive more data from outside



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Rules of thumb:

time-dependent input variable: you must use

an in-connector

changeable constants: you can use an in-connector or DBread block

model-specific information: place inside model but make sure you document it



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Requirements for reusable

model components or MBBs



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reusable in other simulation studies and Extend models

complementary like jigsaw puzzle pieces

self-explaining and well documented (not only in report)

encapsulated, i.e. implementation is hidden

easy to adapt, expand and maintain

manageable in size

constructed following guidelines of Model Delivery System

robust and reliable (i.e. tested for e.g. fool proofness)

scientific maturity



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Typical examples of reusable MBB: standard Extend blocks

clear function – limited nr of connectors - reusable

Plotter block Data fitter block



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Swaney, D.P., Scavia, D., Howarth, R.W., Marino, R.M. (2008) Estuarine classification and response to nitrogen loading: Insights from simple ecological models.

Estuarine Coastal and Shelf Science 77, 253 - 263.



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+ : clear function, limited nr of connectors

- : some changeable parameters in holding tanks

remark: model could allow for variable nr of age classes

note: im- and exporting data slows down your simulation !



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changeable parameters better read from database



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typical example of reuse of a block in a model



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+: limited number of connectors, clear function



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here

documentation

could be added



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-: DB table names

not generic



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SSA Extend models

What material do we have

already to design the MBBs?

-

Some examples



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Catch-effort relationship:



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Two-layer circulation



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Fisheries income:



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Box model for solving 1D advection-diffusion equation:



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Beach attractiveness:



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Eutrophication:



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Estuarine dispersal of N:



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For a tentative list of candidate MBBs: see D8.8 – Appendix A

Please check/complete yourself



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How to do it ?

Deriving the generic MBBs

from your Extend models



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STEP1 Identification ofmodel building

blocksIs the information reusable?

STEP2 Remove model specificparameters and data

Is the block manageablein size?

STEP3 Construct the block

Is the block self explaining?

STEP4 Implement the block

Is the block workingat all times?

Use your model to identify model blocksUse duplicated model patterns to identify model blocksDefine functions of the blocks based on state variables

Put all parameters in the dialogUse connectors for input and output data

Separate data and model

Limit the number of connectors and user defined parameters

Encode in ModL or group generic extend blocks in a H-blockPay special attention to full documentation of the block

Use the guidelines in deliverable D8.4 & D8.8

Testing, testing, testing

Organize sessions with “foolish” test users

yes

yes

yes

no

no

no

no



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Creating a new library : manual p. 494

Note: do not use the name of an existing Extend library



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Suggestion to work with five sublibraries:

economic processes (income, profit etc)

ecological processes (bacterial growth, fish pop dyn)

social & policy processes (attractiveness, policy acceptance etc)

physical processes (diffusion, circulation etc)

non-domain specific tools (integration, regression etc)



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General design recommendations: start with the function of the block: what should it do?

ask yourself: can someone else redesign my model?

limit number of connectors

remove changeable parameters from model

document the block: use the help functionality

separate data and model as much as possible;

use connectors and Extend Database functionality

for details see D8.8



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Extend gives you several ways

to design your model:



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1. Hierarchical or H blocks: can be placed in a library:

fishes/year :

1-group/year :

0-group/year : 0

0

Recruitment:

habitat

g1R

spaw.

T=

km :2 6.7781

g1

fishes

fishes

2-10groups

fishes/year :

Delta pop. : 0

Fishes

kgs

mass/group (0=>10)

fishes/group (0=>10)

See Extend manual, page 540 ff.



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Creating a new H block : manual p. 543



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... or selecting part of your model and making it a H block :



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Opening the structure window (double click + Alt key) you can further design the H block (see page 540 ff):

here more

info could be

added



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After making changes and closing the structure window

Extend will ask how you want to save the H block, for example

in a library or only in your model:



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2. Custom blocks in ModL code: can be placed in a library

NITROGENPRODUCTION

NITROGENPROCESSING

& TRANSPORT COSTS

FARMINGSTATUS

feedback nr farms

feedback area per farm

See Extend manual, page 763 ff.



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advantage: custom-designed user dialogs possible



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3. Single-layer design: intuitive, complete model appears, but cannot be placed in a library (directly):



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4. Using equation boxes :

See Extend manual

p. 68-69, & 601 ff.

note: you can use the comment tab to add info

access to Extend database

possible



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Online Data Portal

-

Model Library



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http://www.spicosa.eu



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For instructions:

see report D9.12 on ftp site (appearing soon)

a detailed manual is in preparation



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Generic data management :

use the Extend Data Base

functionality



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database

level

single column

format for quick

query of data

table

level



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1 Creating a new Extend database



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2 Choosing DB name

3 Adding DB table



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4 Naming DB table 5 Opening DB table viewer



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6 Appending fields (columns)

by double clikcing the records column



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7 Defining the field format



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8 Appending records (rows)



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9 Filling the record with data



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9 Exporting an Extend database to a txt file



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Three different ways to access (massive) data

stored in an Extend database



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1. By means of the Extend DB reading blocks from the value library:



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2. By means of the function DBDataGetAsNumber in an equation block:



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3. By means of DBreading function in a custom-designed block:



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Appraisal Step



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General purpose:

linking science to policy:

how does CZ system respond to policy?



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Appraisal

Linking up the System

Model for Scenario

Assessments

Qualitative Assessments

& Interpretations

Preparation of

Results for Outputs

ESE Assessments

CZ System Model Construction

CZ System Formulations

Quantitative Qualitative

1. Inputs Data &

Key Processes

2. Process & Functional

Component Models

4. ESE

Assessment Plans

3. ESE Models

& Documentation

Formulation



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PrepareESE Models

Interpret ESE Model Results

Run ScenarioSimulations

Construct Simulation Model

Generate Special Products

ESE Models +Scenarios

Complete Interpretive Analyses

Appraisal Sequence Trajectories

5.1

5.2

5.3

Data Archive

Science Report

Model Library

InterpretiveAnalysis Plan

WP4 WP4

WP6 WP9 WP8



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Typical problem when linking the

ESE components:

how to combine different time steps ?

several solutions

recommendation: use smallest time step

(see page 83 of Extend manual)



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The Extend – PCRaster interface :

a quick outlook



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How will it work ? Level 3 interface by means of

custom-designed Extend block PCRstep:

1. Extend writes data for PCRaster to txt file

2. Extend writes lockfile (to keep it from running)

3. Extend starts PCRaster

4. PCRaster runs, writes data for use by Extend.

5. PCRaster removes lockfile

6. Extend continues

7. Model goes to step 1



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Extend interface block PCR Step :



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When will it be available?

demo of first version during next SAF meeting mid June

calibrated version + PCRaster workshop for sites that are ready by the end of 2009



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Workshop schedule:

following break-out groups to discuss model-specific

issues related to the library design and review

Group A: SSAs .....

Group B: SSAs ....

Group C: SSA

........



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In summary:

restructure your Extend models

define the function of reusable blocks

pay attention to data management + documentation

implement selection of model as hierarchical H block

save in custom Extend library (see page 547 of manual)

delivery to Data Portal (follow guidelines of WP9)



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QUESTIONS ?

Jean-Luc de Kok Flemish Institute for Technological Research (VITO)

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