cellular automata bioremediation bioremediation system system cellular automata bioremediation...

Cellular AutomataCellular Automata BIORemediationBIORemediation

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Cellular AutomataCellular Automata BIORemediationBIORemediation

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M.C.Baracca P.Ornelli G.ClaiENEA Italy

M.C.Baracca P.Ornelli G.ClaiENEA Italy

The Esprit HPCN Colombo Project consortiumThe Esprit HPCN Colombo Project consortium

• CRA Montecatini: a private italian group involved in polluted soil reclamation.

• Umweltschutz Nord: the largest german soil remediation company.

• Ironside Farrar: Scotlands leading environmental consultants.

• ENEA-HPCN: The High Performance Computing group of the Italian National Agency for New Technologies, Energy and Environment

• EPCC: the Edinburgh University parallel computing centre.

• ISI-CNR: The Computer Science Institute of the Italian National Research Centre.

• UNICAL: the Department of Mathematics at Calabria University in Italy.

• QSW: a European parallel computers supplier.

The Colombo Project

CAMELotparallel environmentfor CA based models

Cabiorgraphical packagefor bioremediation

intervention simulation

In situ bioremediationCA based modelCA Modelists Bioremediation users

The Bioremediation ModelThe Bioremediation ModelThe Bioremediation ModelThe Bioremediation Model

• Multiphase (water, air,pollutant) flow in a porous saturated or unsaturated soil

• Solute transport, adsorption/desorption• Chemical reactions• Biomass growth and interaction with contaminants

and nutrients

The CA Bioremediation codeThe CA Bioremediation code

• 3D automaton• each cell interacting with 8 neighbouring cells• 185 general parameters• cell state defined by 86 substates• simulation evolution managed by a computational

steering mechanism

CAMELot environmentCAMELot environment

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Master process

Process

Process

Process

MP I

CA Engine

User Interface

Edit

Compile

BuildRun Transition function

Cabior systemCabior system

Postprocessing

Simulation Optimization

Cabior MainCabior MainWindowWindow

Pilot Plant Real Field

Model Tuning

Simulationperiodicoutcome

CA Preprocessing

Cabior sw overviewCabior sw overviewCabior sw overviewCabior sw overview

• Based on AVS/Express 5.0• built both connecting and customizing appropriate

AVS components and developing some new modules

• developed on SGI Onyx2 platform• ported on PC cluster running Linux and compiled

with LessTif freeware library

Preprocessing overviewPreprocessing overviewPreprocessing overviewPreprocessing overview

• It assists the user allowing the visualization, while editing, of the binary input files required by the bioremediation simulation.

• It supports the definition of the automaton general characteristic (dimensions, cell sizes, the real time to be simulated ….).

• It permits to prepare all those files defining the state of each cell ( substates), providing the modalities to represent both homogeneous cell array and discontinuities like surfaces and lateral walls, injection and extraction wells.

• It allows to import binary files coming from platforms with incompatible binary formats.

Optimization methods

Cellular Automaton

Fitness evaluation

dataexperiments

Soilplant

Best

AutomatonCellular

Pilot FITNESS:

2

1

N

i i

ii

real

simulatedrealf

Time Target

t1 Y1

t2 Y2

t3 Y3

t4 Y4

…tN YN

Model parameters tuningModel parameters tuningModel parameters tuningModel parameters tuning

Edit Experimental DataEdit Experimental Data

Optimization flow

OptimizationGraphicalInterface

Optimization

Procedure

( batch )

OptimizationAlgorithm

Fitnessevaluation

Proposed newparameters

Bioremediationapplication

Calculatedresults

ExperimentalData file

New inputfile

Endconditionnn

User settings memorization

Proposedsolution

Yes

Optimization FlowOptimization FlowOptimization FlowOptimization Flow

Postprocessing overviewPostprocessing overviewPostprocessing overviewPostprocessing overview

• To perform 3D visualization of the substates of the automaton using different geometrical modalities;

• to show the substate value and the coordinates of a single cell;

• to visualize the temporal evolution of a substate, according to a chosen geometrical modality;

• to visualize vectorial fields.

Postprocessing applicationPostprocessing applicationPostprocessing applicationPostprocessing application

• AVS/Express Single Window Application;• the visualization window is composed of:

- the Visualization space

- the Application Modules space• the data files to be visualized are retrieved by

means of specific descriptors produced together with the simulation output.