DosiVox

DosiVox (version 1.0) is a free software (GNU GPL-3 licence, see above) based on the Geant4 C++ libraries (Agostinelli et al., 2003; Allison et al., 2006; Allison et al., 2016) and responding to the Geant4 Software Licence (version Geant4 10.1). It is developed by L. Martin, N. Mercier and S. Incerti at the IRAMAT-CRP2A[1] and the CENBG[2]. DosiVox allows constructing of voxelised models of archaeological objects and simulating the radioactivity for dose calculation with a Monte-Carlo approach (Martin et al., 2015a; Martin et al., 2015b; Martin 2015). These dose calculations can be used in the context of trapped charge dating. DosiVox uses Pilot Text Files (PTF) to set the simulation geometry and parameters, allowing the creation of a simulation by writing or editing a text file -> no skill in programming nor in Geant4 is required.

DosiVox runs on a Linux system and was developed on a Scientific Linux (Red Hat) virtual machine available at http://geant4.in2p3.fr/spip.php?rubrique8. As explained in Martin (2015): the alpha particle spectra (U_alpha, Th_alpha) are constructed from the NIST online database (version 5.0.0, October 2012; Kramida et al., 2018); the beta particle spectra (Ubeta, Thbeta, Kbeta) and the gamma particle spectra (Ugamma, Thgamma) are based on the data from the NNDC (Brookhaven National Laboratory, USA http://www.nndc.bnl.gov) online database NuDat (version November 2009). In addition, the K gamma spectra (Kgamma) are constructed from NNDC online database NuDat (version January 2013; Kinsey et al., 1996).

Installation

You can download the software as a zip from this URL.

To download the package source as you see it on GitHub, for offline browsing, use this line at the shell prompt (assuming you have Git installed on your computer):

git clone https://github.com/crp2a/DosiVox.git

Extract the archive of your home folder. Run the Scientific Linux virtual machine in a Windows or OS-X operating system and extract the archive in the virtual machine's Home folder. More explanations are available in the DosiVox Installation Guide.

Usage

Setting a simulation with PTF

Modify any PTF present in the DosiVox/data folder respecting the file's layout. The texts after the "#" symbol are comments describing the data of the line. All data must be separated by at least a space. Do not add a supplementary line unless it corresponds to data in agreement with the PTF layout. Detailed explanations are available in the DosiVox Manual.

Launch a simulation in DosiVox

Open a terminal localised in the DosiVox/ folder. Detailed explanations are available in the DosiVox Manual.

Basic Commands

Run DosiVox (in a terminal open in the DosiVox/ folder)

Run DosiVox without visualisation:

build/DosiVox

Run the basic visualisation tool of DosiVox:

build/DosiVox vis.mac

Run the visualisation of the DosiVox tool with the detectors displaying:

build/DosiVox visdet.mac

WARNING: the displaying of detectors composed of a lot of geometrical elements can be costly for the computer resources

Use Ctrl + C to abort the running simulation.

Run DosiVox under the DosiVox visualisation tool (in the "Session" box of the visualisation tool)

Run the simulation in the visualisation tool:

control/execute 1run.mac

WARNING: to avoid over-consumption of the computer resources, the run under the visualisation tool is limited to 1000 particles emitted

Exit the visualisation tool (it will exit the DosiVox session too):

exit

To move the displayed model, use the mouse left and scroll buttons on the display window and the keyboard arrows.

Results

Results of simulations are written as text files in the DosiVox/results folder with the prefix defined in the corresponding PTF. Suffixes corresponding to the detector and data type are added to the results files:

• _error for the listing of the killed particles,
• _probe for the recording of the probe detector,
• _detectorN for the N detector (N=1-> sub-voxelised, N=2-> single grain packing, N=3-> successive grain packings),
• _grains for the dose for each grain for detector 2 or 3. For detector 1, a 3D mapping is written as a text file in the DosiVox/results/DoseMapping folder.

These results text files can be opened with standard spreadsheets. Detailed explanations are available in the DosiVox DosiVox Manual.

Examples of PTF

Some examples of PTF are provided with DosiVox, in the DosiVox/data folder:

• XPL0 creates two voxels filled respectively with clay and quartz. It simulates the alpha radioactivity of the U-series in the clay, allowing to record of the dose attenuation in the quartz with the probe detector.
• XPL1 is a PTF for creating a simple voxelisation as a 3 x 3 x 3 grid and only the probe detector. Beta particles of the U-series are simulated.
• XPL1bis creates a similar model than XPL1, but with a 20 x 20 x 20 grid.
• XPL2 creates a 20 x 20 20 voxels model with water, air and sediment-type materials to simulate gamma particles. Only the probe detector is defined
• XPL3 defines a single random packing of grains as a detector in a 20 x 20 x 20 grid, in addition to the probe detector. Beta particles of the Th-series are simulated.
• XPL3bis uses the same configuration as XPL3 but creates successive random packings of grains as detectors.
• XPL4 defines a sub-voxelisation of 20 x 20 x 20 as detector in a voxel of the main 20 x 20 x 20 grid. Alpha particles of the U-series are simulated in this model.
• XPL5 used the sub-voxelised detector to model a flint in a 120 x 250 x 101 sub-voxels grid. Beta particles of the U-series are simulated, and only the doses in the sub-voxels representing the flint are mapped.

Detailed explanations are available in the DosiVox Manual.

technical support

• Loïc MARTIN
• Norbert MERCIER

References

Agostinelli et al., 2003. Geant4—a simulation toolkit. Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, 506. https://doi.org/10.1016/S0168-9002(03)01368-8

Allison et al., 2006. Geant4 developments and applications. IEEE Transactions on Nuclear Science 53. https://doi.org/10.1109/TNS.2006.869826

Allison, J., et al., 2016. Recent developments in Geant4. Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment 835, 186-225. https://doi.org/10.1016/j.nima.2016.06.125

Martin, L., Incerti, S., Mercier, N., 2015a. DosiVox: Implementing Geant 4-based software for dosimetry simulations relevant to luminescence and ESR dating techniques. Ancient TL, 33(1). http://ancienttl.org/ATL_33-1_2015/ATL_33-1_Martin_p1-10.pdf

Martin, L., Mercier, N., Incerti, S., Lefrais, Y., Pecheyran, C., Guerin, G., Jarry, M., Bruxelles, L., Bon, F., Pallier C., 2015b. Dosimetric study of sediments at the Beta dose rate scale: characterisation and modelisation with the DosiVox software. Radiation Measurement, 81, 134-141. https://doi.org/10.1016/j.radmeas.2015.02.008

Kinsey, R. R., Dunford, C. L., Tuli, J. K., Burrows, T. W., 1996. The NUDAT/PCNUDAT Program for Nuclear Data. 9th International Symposium of Capture Gamma-Ray Spectroscopy and Related Topics (Budapest, Hungary; October 1996). Data extracted from the NUDATdatabase, version Nov 2009 and Jan 2013 https://www.nndc.bnl.gov/nudat2/reCenter.jsp?z=50&n=63

Kramida, A., Ralchenko, Yu., Reader, J., NIST ASD Team, 2018. NIST Atomic Spectra Database (version 5.0.0) https://physics.nist.gov/asd [Nov 2012]. National Institute of Standards and Technology, Gaithersburg, MD. https://doi.org/10.18434/T4W30F

Martin, L., 2015. Caractérisation et modélisation d'objets archéologiques en vue de leur datation par des méthodes paléo-dosimétriques : simulation des paramètres dosimétriques sous Geant4. Thèse de doctorat en Physique des archéomatériaux. Pessac: Université Bordeaux-Montaigne, 304p. http://www.theses.fr/2015BOR30055

Rasband, W. S., 1997-2012. ImageJ, U.S. National Institutes of Health, Bethesda, Maryland, USA. https://imagej.nih.gov/ij/

Schneider, C. A., Rasband, W. S., Eliceiri, K. W., 2012. NIH Image to ImageJ: 25 years of image analysis. Nature Methods, 671. https://doi.org/10.1038/nmeth.2089

License

DosiVox is provided under the terms and conditions of the DosiVox Software License (GNU GPL-3).

Neither the authors of this software system, nor their employing institutes, nor the agencies providing financial support for this work make any representation or warranty, express or implied, regarding this software system or assume any liability for its use. Please see the LICENSE file for the full disclaimer and the limitation of liability.

By using, copying, modifying or distributing the software (or any work based on the software), you agree to acknowledge its use in resulting acceptance of all terms of the DosiVox Software license.

1. Institut de Recherche sur les ArchéoMATériaux - Centre de Recherche en Physique Appliquée à l'Archéologie http://www.iramat-crp2a.cnrs.fr
2. Centre d'Etudes Nucléaires de Bordeaux Gradignan http://www.cenbg.in2p3.fr