|Message: Re: Coral optical model (3D)||Not Logged In (login)|
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> I would like to do a 3D model for a sclerantininan coral to study its > interaction with light. In particular I interested in understand the > influence of the geometry of the skeleton in the algae absorption. I > think Geant4 could be very helpful to address this problem and greatly > appreciate your advice and recommendations.
Geant4 has myriad ways of defining geometry objects and although I don't know exactly how involved your 3D model is I'd ventrue to say that it can be implemented in Geant4. From a quick look at your paper I see that you have an infinite periodic pattern and that therefore a trick is necessary when the track leaves on end for it to wrap around to the beginning. I know this problem has been solved in other G4 application, and it is relatively easy to solve, but there is no automated mechanism in G4 for this be done without user intervention - as far as I know.
> The geometry of a coral can be very complex, but it could start with a > simple geometry such as the fungi coral, which could be modeled in a > very simple way as a collection of cylinders lying down around a central > point.
Should be "easy" (after some initial learning curve)
> Actually we have done a 2D model ( > http://dx.doi.org/10.1364/AO.49.005032 ) with a Monte Carlo simulation > (MCML, Multi Carlo Multi Layered). For this we had to build experimental > arrangements and methods for estimating inherent optical properties > (absorption and scattering coefficients and anisotropy parameter) for > the coral skeleton and the micro algae.
Optical modeling in G4 depends greatly on your knowledge of empirical optical parameters. If you already know them, those can be fed to G4. Optical surfaces are defined in G4 between 'volumes' (border-surface) or around a 'volume' (skin-surface). Geometries are 'constructed' like a Matryoshka doll with daughter volumes inside 'mother volumes'. Surfaces can be between flush daughters or between the daughter and the mother. Volumes are filled with material which have bulk optical properties.
> These optical characterization methods could also be used to > characterize optically sliced turbid media or microparticle suspensions.
Currently, the index of refraction cannot continuously vary within a volume. Each region with a different index must be defined as separate volumes. These volumes can be small and random (I have seen an implementation where a user defines a medium made of random size sand spheres randomly filling a vial) but that geometry must be coded by the user.
The scattering length in a medium is set by the user. Mie and Rayleigh scattering processes are available.
> Which could serve to increase the database of the optical properties of > Geant4.
The G4 toolkit does not come with a database for optical properties except for Look-Up-Tables (LUT) containing measured optical reflectance for a variety of surface treatments.
Best regards, Peter
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