Introduction

The Cabior system is devoted to the needs of the bioremediation user which generally is not skilled enough in modelling or in computer science, so it has been designed in order to hide as many computational technical details as possible and at the same time to provide advanced features to analyze and to test the model outcome.

It has been developed by means of AVS/Express a comercial visualization package, portable across several platforms of industrial interest, that provides the graphical primitives allowing a sophisticated data visualization.

The Cabior system consists in a graphical environment allowing to enter the pre-processing and post-processing facilities as well as to run the batch simulation and the parameters optimization algorithms.

- Cabior Main Window -

In the following sections the features and the functionalities provided by the Cabior system are briefly summarized. More detailed information can be found at the web site: http://eboals.bologna.enea.it/colombo

The graphical pre-processing tool assists the user during the preparation of input data since it allows the visualization, while editing, of the input data files required by CAMELot environment and the transition function simulating the bioremediation intervention. The input data files are of two different kinds: one describing the general automaton characteristcs and several other files representing the automaton substates, that is the variables defining the state of each cell.

The general characteristics of the automaton can be set or modify by means of the General Parameters Menu while the Parameters Set Menus allow the separated input of the simulation parameters referred to each of the specific bioremediation layers.

Automation General Parameters Menu-

Pressing the Edit.cmt button, a further panel opens for the editing of 1-2-3D automaton substates with the possibility to combine a random or constant initialization of the cell values with the single cell value setting, in order to easily initialize homogeneous cells arrays and discontinuities like surfaces, lateral walls, injection and extraction wells. Relevant to the user is the panel capability to show the numerical cell values of a chosen automaton plane simultaneously with its discrete visualization according to the colormap at the bottom of the window.

Substates Editor

The aim of the post-processing 3D visualization is to perform a detailed analysis of the data gathered during the simulation in order to obtain meaningful insights into simulation results. Using this tool, a bioremediation user may analyze, study and discover useful features and numerical results that cannot be discovered during the simulation.

Its main features can be summarized as follows:

• to visualize 3D data sets in a 3 dimensional space, using different geometrical modalities like orthoslices, isosurfaces, isovolumes and volumes of cells whose values range in a chosen interval (Bounded volume feature);
• to rotate, to translate, to scale and to zoom the picture;
• to show the substate value and the coordinates of a single cell simply clicking on the image in the Visualization space (Probe feature);
• to visualize vectorial fields;
• to visualize the temporal evolution of a substate, according to a chosen geometrical modality, using a sequence of snapshots taken during the simulation at different steps.

Orthoslices and Probe feature

Moreover, the isosurface modality has been improved not only allowing to visualize a surface of a given constant value level in the selected substate as you saw in the demo at the review meeting but including also the opportunity to map on a substate isosurface the cell values of another substate.

A further requirement has arisen from the analysis of the bioremediation model application to real field: the surface dimensions are much larger than the field depth, so that the automaton cell looks like a parallelepiped and not a cube.

In order to properly visualize the automaton in this case, the Scale module, allowing   to choose and set a different scale on each axis, has been introduced.

The Scale factor affect at the same time the scalar substate as well as the vector fields, so that in case of a superposition of a substate and a vector field, changing the Scale factor the whole image changes accordingly.  

The Cabior user can start the bioremediation simulation in batch mode by means of the window shown here below.

This window simply requires the user to choose the input files following the CAMELot files name convention and to set the number of iteration to be run, the saving period, the output files name and the number of processes to handle the task, while hiding the practical issues to obtain the executable and then run it on the underlying parallel architecture .

The aim of this panel is to produce the simulation outputs related to specified time periods which could be visualized subsequently by means of post-processing tool.

In the model there are some parameters which cannot be directly determined, so that their values will be adjusted by comparing the model outcome with a set of experimental data.

The basic idea is that it is possible to tune these parameters using experimental data resulting from small scale tests, and that they could be succesfully applied on a much larger scale simulation.

The optimization procedure applied to bioremediation simulation results, interacts with the simulation code as sketched below:

The optimization sequence panels permit to choose the optimization technique ( Genetic Algorithm or Simulated Annealing ) , to turn on the model parameters suitable for optimization, to set the parameters required by the method itself, to input the experimental data file and finally to run the optimization procedure.