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1. Remote Sensing Based Land Cover Map of Watersheds in the Swedish Arctics: Study of Spatial and Temporal Variabilities of Land Cover

Author

Yves AUDA Auda, Erik J. Lundin, David Gustafsson, Oleg S. Pokrovsky, Simon Cazaurang, and Laurent Orgogozo

Abstract

A land cover map of two arctic catchments, nearby the Abisko Scientific Research Station, was obtained from a classification of a Sentinel-2 satellite image and a ground survey performed in July 2022. The two contiguous catchments, Miellajokka and Stordalen, are covered by various ecotypes, from boreal forest to alpine tundra and peatland. The Random Forest algorithm correctly identified 83% of polygon pixels reserved for testing. The developed workflow relied solely on open source software and acquired ground observations. Space organization was directed by the altitude as shown by the intersection of the land cover with the topography. Comparison between this new land cover map and previous ones based on data acquired between 2008 and 2011 demonstrates some trends of vegetation cover evolution in response to climate change in the considered area. The potential applications in terms of permafrost modeling (hiperborea.omp.eu) are finally discussed.

Published
2023
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2. Numerical Assessment of Morphological and Hydraulic Properties of Moss, Lichen and Peat from a Permafrost Peatland

Author

Simon Cazaurang, Manuel Marcoux, Oleg S. Pokrovsky, Sergey V. Loiko, Artem G. Lim, Stéphane Audry, Liudmila S. Shirokova, Laurent Orgogozo, Institut de mécanique des fluides de Toulouse (IMFT), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT), Géosciences Environnement Toulouse (GET), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Tomsk State University [Tomsk], N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch (FECIAR UrB RAS ), Russian Academy of Sciences - Chernogolovka, and ANR-19-CE46-0003,HiPerBorea,Calul haute performance pour la quantification des impacts du changement climatique sur les régions boréales(2019)

Subjects
[PHYS]Physics [physics], Peatland, [SDU]Sciences of the Universe [physics], Hydraulic conductivity, [SDE]Environmental Sciences, Porous media, Permafrost, General Earth and Planetary Sciences, Lichen, [INFO]Computer Science [cs], Computational fluid dynamics, Moss, General Environmental Science
Abstract

Due to its insulating and draining role, assessing ground vegetation cover properties is important for high-resolution hydrological modeling of permafrost regions. In this study, morphological and effective hydraulic properties of Western Siberian Lowland ground vegetation samples (lichens, Sphagnum mosses, peat) are numerically studied based on tomography scans. Porosity is estimated through a void voxels counting algorithm, showing the existence of representative elementary volumes (REVs) of porosity for most samples. Then, two methods are used to estimate hydraulic conductivity depending on the sample's homogeneity. For homogeneous samples, direct numerical simulations of a single-phase flow are performed, leading to a definition of hydraulic conductivity related to a REV, which is larger than those obtained for porosity. For heterogeneous samples, no adequate REV may be defined. To bypass this issue, a pore network representation is created from computerized scans. Morphological and hydraulic properties are then estimated through this simplified representation. Both methods converged on similar results for porosity. Some discrepancies are observed for a specific surface area. Hydraulic conductivity fluctuates by 2 orders of magnitude, depending on the method used. Porosity values are in line with previous values found in the literature, showing that arctic cryptogamic cover can be considered an open and well-connected porous medium (over 99 % of overall porosity is open porosity). Meanwhile, digitally estimated hydraulic conductivity is higher compared to previously obtained results based on field and laboratory experiments. However, the uncertainty is less than in experimental studies available in the literature. Therefore, biological and sampling artifacts are predominant over numerical biases. This could be related to compressibility effects occurring during field or laboratory measurements. These numerical methods lay a solid foundation for interpreting the homogeneity of any type of sample and processing some quantitative properties' assessment, either with image processing or with a pore network model. The main observed limitation is the input data quality (e.g., the tomographic scans' resolution) and its pre-processing scheme. Thus, some supplementary studies are compulsory for assessing syn-sampling and syn-measurement perturbations in experimentally estimated, effective hydraulic properties of such a biological porous medium.

Published
2022
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3. Fractionation of Organic C, Nutrients, Metals And Bacteria In Peat Porewater And Ice After Freezing And Thawing

Author

Sergey Yu Morgalev, Artem G. Lim, Tamara G. Morgaleva, Yuri N. Morgalev, Rinat M. Manasypov, Daria Kuzmina, Liudmila S. Shirokova, Laurent Orgogozo, Sergey V. Loiko, and Oleg S. Pokrovsky

Subjects
замерзание, микроорганизмы, оттаивание, токсичные вещества, Health, Toxicology and Mutagenesis, поровые воды, торф, Environmental Chemistry, General Medicine, основные микроэлементы, питательные вещества, Pollution
Abstract

To better understand freezing - thawing cycles operating in peat soils of permafrost landscapes, we experimentally modelled bi-directional freezing and thawing of the three sections of 90-cm long peat core collected from a discontinuous permafrost zone in western Siberia. We measured translocation of microorganisms and changes in porewater chemistry (pH, UV absorbance, dissolved organic carbon (DOC), and major and trace element concentrations) after thawing and two-way freezing of peat cores. We demonstrate that bi-directional freezing and thawing of a peat core is capable of strongly modifying the vertical pattern of bacteria, DOC, nutrients, and trace element concentrations. Sizeable enrichment (a factor of 2 to 5) of DOC, macro- (P, K, Ca) and micro-nutrients (Ni, Mn, Co, Rb, B) and some low-mobile trace elements in several horizons of ice and peat porewater after freeze/thaw experiment may stem from physical disintegration of peat particles, leaching of peat constituents and opening of isolated (non-connected) pores during freezing front migration. However, due to the appearance of multiple maxima of element concentration after a freeze-thaw event, the use of peat ice chemical composition as environmental archive for paleo-reconstructions is unwarranted.

Published
2022
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4. RichardsFoam3: A new version of RichardsFoam for continental surfaces hydrogeology modelling

Author

Laurent Orgogozo, Géosciences Environnement Toulouse (GET), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), and ANR-19-CE46-0003,HiPerBorea,Calul haute performance pour la quantification des impacts du changement climatique sur les régions boréales(2019)

Subjects
Source lines of code, Source code, Discretization, Computer science, media_common.quotation_subject, Infiltration, General Physics and Astronomy, Richards equation, Exfiltration, Solver, Numbering, Computational science, Hardware and Architecture, Linearization, Hydrogeological modelling, [SDU]Sciences of the Universe [physics], OpenFOAM®, Massively parallel, media_common
Abstract

RichardsFoam3 is an updated version of the OpenFOAM® solver RichardsFoam, previously presented in “An open source massively parallel solver for Richards equation: Mechanistic modelling of water fluxes at the watershed scale” by L. Orgogozo, N. Renon, C. Soulaine, F. Henon, S.K. Tomer, D. Labat, O.S. Pokrovsky, M. Sekhar, R. Ababou, M. Quintard (Comput. Phys. Commun. 185 (2014) 3358-3371, https://doi.org/10.1016/j.cpc.2014.08.004 ), and in the new version announcement “RichardsFOAM2: a new version of RichardsFOAM devoted to the modelling of the vadose zone” by L. Orgogozo (Comput. Phys. Commun. 196 (2015) 619-620, https://doi.org/10.1016/j.cpc.2015.07.009 ). This new version includes improvements of memory handling and of on-the-fly control of computations, a better integration in the OpenFOAM® framework, simplifications of the coding of some expressions, as well as new advanced boundary conditions. All together these developments allow to enhance the ease of application of the code to continental surfaces hydrogeology modelling, its computational performances and its readability. The description of the elements contained in this release may be found in the readMe file. Please note that you may also find RichardsFoam3 on the hydrology page of the develop.openfoam.com interface: https://develop.openfoam.com/Community/hydrology/ New version program summary Program title: RichardsFoam3 CPC Library link to program files: https://doi.org/10.17632/vkr7sd6fhb.1 Developer's repository link: https://develop.openfoam.com/Community/hydrology/ Licensing provisions: GPLv3 Programming language: C++ Supplementary material: The full system of equations solved by RichardsFoam3 is presented in the documentation directory of the RichardsFoam3 package, with a numbering that is used in the comments of the main source file RichardsFoam3.C of the solver RichardsFoam3, in order to identify which lines of code are related to which equation. Journal reference of previous version: Comput. Phys. Commun. 196 (2015) 619-620 Does the new version supersede the previous version?: Yes Reasons for the new version: Introducing new functionalities and implementing improvements for ergonomy, computational performances and readability Summary of revisions: The new features compared to RichardsFOAM [1] and RichardsFoam2 [2] are the following: (i) better handling of memory use during computation; (ii) possibility of on-the-fly modification of the control parameters of the linearisation procedure; (iii) new boundary conditions to be compiled along with the solver itself, and dedicated to the simulation of rain infiltration (rainFallFlux) or no infiltration (noFlux) conditions while allowing exfiltration with OpenFOAM® stand-alone (i.e. without mandatory use of swak4foam as it was the case in RichardsFoam2 [2]); (iv) Computation of the field of piezometric head along computation. NB: in the demonstration cases, a way to implement a constant piezometric head boundary conditions with OpenFOAM is proposed. (v) new functions that allow to build seasonally variable boundary conditions easily; (vi) use of postprocessing procedures with OpenFOAM® stand-alone (i.e. without mandatory use of swak4foam as it was the case in RichardsFoam2 [2]); (vii) several other minor rewritings/cleanings of the code. Nature of problem: This software solves the non-linear three-dimensional transient Richards equation, which is a very popular model for water transfer in variably saturated porous media (e.g.: soils). It is designed to take advantage of the massively parallel computing performance of OpenFOAM®. The goal is to be able to model natural hydrosystems on large temporal and spatial scales. Solution method: A mixed implicit (FVM in the object oriented OpenFOAM framework) and explicit (FVC in the object oriented OpenFOAM® framework) discretization of the equation with a backward time scheme is coupled with a linearization method (Picard algorithm). Due to the linearization loop the final solution of each time step tends towards a fully implicit solution. The implementation has been carried out with a concern for robustness and parallel efficiency. References [1] L. Orgogozo, N. Renon, C. Soulaine, F. Henon, S.K. Tomer, D. Labat, O.S. Pokrovsky, M. Sekhar, R. Ababou, M. Quintard, An open source massively parallel solver for Richards equation: mechanistic modelling of water fluxes at the watershed scale, Comput. Phys. Commun. 185 (2014) 3358–3371, https://doi.org/10.1016/j.cpc.2014.08.004 . [2] L. Orgogozo, RichardsFOAM2: a new version of RichardsFOAM devoted to the modelling of the vadose zone, Comput. Phys. Commun. 196 (2015) 619–620, https://doi.org/10.1016/j.cpc.2015.07.009 .

Published
2022
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5. Contribution of soil elemental contents and Cu and Sr isotope ratios to the understanding of pedogenetic processes and mechanisms involved in the soil-to-grape transfer (Soave vineyard, Italy)

Author

Giuseppe D. Saldi, Jérôme Viers, Laurent Orgogozo, Eva Schreck, José Darrozes, Simon Blotevogel, Priscia Oliva, Pierre Courjault-Radé, Stéphane Audry, Géosciences Environnement Toulouse (GET), Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), and Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS)

Subjects
Mineral nutrition, Soil Science, 010501 environmental sciences, [CHIM.INOR]Chemical Sciences/Inorganic chemistry, 01 natural sciences, Vineyard, [CHIM.ANAL]Chemical Sciences/Analytical chemistry, [SDU.STU.GC]Sciences of the Universe [physics]/Earth Sciences/Geochemistry, Vineyard soil, 0105 earth and related environmental sciences, 2. Zero hunger, Radiogenic nuclide, Chemistry, Soil chemistry, Soil classification, 04 agricultural and veterinary sciences, [CHIM.MATE]Chemical Sciences/Material chemistry, 15. Life on land, Soil type, Element transfers, Soil formation, Isotopes of carbon, Environmental chemistry, Soil water, [SDE]Environmental Sciences, 040103 agronomy & agriculture, Sr and Cu isotopes, 0401 agriculture, forestry, and fisheries, Calcareous
Abstract

International audience; The effect of soil on wine composition and flavor is controversially discussed in viticulture. Mineral nutrition of the grapevine is one possibility for an influence of soil chemistry on winemaking. However, effects of soil chemistry are difficult to isolate from other physical and biological factors.Here two winegrowing plots in the Soave region (Italy) were investigated, lying side by side on contrasted soil types. Factors that influenced soil formation and characterize soil chemistry and mineralogy were determined. The influence of soil type on the elemental composition (Mg, Al, P, S, K, Ca, Mn, Fe, Cu, Zn, Sr, Mo and Ba) of leaves and grapes was studied. Carbon isotope ratios were measured to evaluate water stress. Radiogenic Sr and stable Cu isotope ratios were studied to identify the influence of different bedrocks and better understand the mechanisms involved in the soil-to-grape continuum.Even though the morphology of soils is different, chemical characteristics are similar in both vineyard plots. Nevertheless, Sr isotope ratios of horizons of both soils show influence of different bedrocks on their genesis. The composition of grapevine plants is similar between both plots even though there is a tendency for higher elemental contents on more calcareous soil. Finally, isotope ratios show that different mechanisms control Cu and Sr in plant: Cu seems to be controlled by regulation mechanisms of the plants whereas Sr is absorbed in ratios similar to the soil, reflecting the different geological origins.

Published
2019
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6. Water and energy transfer modeling in a permafrost‐dominated, forested catchment of Central Siberia: the key role of rooting depth

Author

Anatoly S. Prokushkin, Laurent Orgogozo, Oleg S. Pokrovsky, Jérôme Viers, Stéphane Audry, Michel Quintard, Christophe Grenier, Géosciences Environnement Toulouse (GET), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), V.N. Sukachev Institute of Forest, Siberian Branch of the Russian Academy of Sciences (SB RAS), Tomsk State University [Tomsk], Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Modélisation Hydrologique (HYDRO), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut de mécanique des fluides de Toulouse (IMFT), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT), Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées, Laboratoire des Mécanismes et Transfert en Géologie (LMTG), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Commissariat à l'Energie Atomique et aux énergies alternatives - CEA (FRANCE), Centre National d'Études Spatiales - CNES (FRANCE), Centre National de la Recherche Scientifique - CNRS (FRANCE), Institut National Polytechnique de Toulouse - INPT (FRANCE), Institut de Recherche pour le Développement - IRD (FRANCE), Université Toulouse III - Paul Sabatier - UT3 (FRANCE), Université de Versailles Saint-Quentin-en-Yvelines -UVSQ (FRANCE), Bureau de Recherches Géologiques et Minières - BRGM (FRANCE), V. N. Sukachev Institute of Forest (RUSSIA), Tomsk State University - TSU (RUSSIA), Laboratoire des Sciences du Climat et de l'Environnement - LSCE (Gif-sur-Yvette, France), Institut National Polytechnique de Toulouse - Toulouse INP (FRANCE), and Université de Toulouse (UT)-Université de Toulouse (UT)-Observatoire Midi-Pyrénées (OMP)

Subjects
Biogeochemical cycle, Watershed, 010504 meteorology & atmospheric sciences, Mécanique des fluides, [SDE.MCG]Environmental Sciences/Global Changes, 0207 environmental engineering, Drainage basin, Active layer dynamics, Permafrost, 02 engineering and technology, Atmospheric sciences, 01 natural sciences, Hydrology (agriculture), Evapotranspiration, Fluid dynamics, ACM: I.: Computing Methodologies/I.6: SIMULATION AND MODELING/I.6.5: Model Development, OpenFOAM, OpenFOAM®, [PHYS.MECA.MEFL]Physics [physics]/Mechanics [physics]/Fluid mechanics [physics.class-ph], [SDU.STU.HY]Sciences of the Universe [physics]/Earth Sciences/Hydrology, 020701 environmental engineering, [SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces, environment, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences, Earth-Surface Processes, geography, geography.geographical_feature_category, Permafrost modeling, [SDE.IE]Environmental Sciences/Environmental Engineering, 15. Life on land, cryohydrogeology modeling, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, 13. Climate action, Soil water, [PHYS.MECA.THER]Physics [physics]/Mechanics [physics]/Thermics [physics.class-ph], Massively parallel computation, Cryohydrogeology modelling, Geology
Abstract

International audience; In order to quantify the impact of evapotranspiration phenomena on active layer dynamics in a permafrost-dominated forested watershed in Central Siberia, we performed a numerical cryohydrological study of water and energy transfer using a new open source cryohydrogeology simulator, with two innovative features: the spatially distributed, mechanistic handling of evapotranspiration and the inclusion of the developed numerical tool in the high performance computing tool box for numerical simulation of fluid dynamics OpenFOAM®. In this region, the heterogeneity of solar exposure leads to strong contrasts in vegetation cover, which constitute the main source of variability of hydrological conditions at the landscape scale. The uncalibrated numerical results reasonably reproduce the measured soil temperature profiles and the dynamics of infiltrated waters revealed by previous biogeochemical studies. The impacts of the thermo-hydrological processes on the water fluxes from the soils to the stream are discussed through comparison between numerical results and field data. The impact of evapotranspiration on water fluxes is studied numerically, which highlights a strong sensitivity to the variability of rooting depth and corresponding evapotranspiration at the slopes of different aspects in the catchment.

Published
2019
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7. Groundwater flow and heat transport for systems undergoing freeze-thaw : Intercomparison of numerical simulators for 2D test cases

Author

N. Collier, Andrew Frampton, Agnès Rivière, Johann Holmén, Emmanuel Mouche, John Molson, Barret L. Kurylyk, Ethan T. Coon, Jennifer M. Frederick, René Therrien, Patrik Vidstrand, Jan Olof Selroos, Clifford I. Voss, Romain Pannetier, Nicolas Roux, Christophe Grenier, Quentin Chanzy, Laurent Orgogozo, Samuel Kokh, Johanna Scheidegger, H. Anbergen, François Costard, Wolfram Rühaak, Victor F. Bense, Michel Ferry, Julio Gonçalvès, Anne Jost, Jeffrey M. McKenzie, Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Modélisation Hydrologique (HYDRO), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), APS Antriebs-, Prüf- und Steuertechnik GmbH, School of Environmental Sciences [Norwich], University of East Anglia [Norwich] (UEA), ENS Cachan, Département Génie Mécanique, Université Paris-Saclay, Cachan, France, Los Alamos National Laboratory (LANL), Oak Ridge National Laboratory [Oak Ridge] (ORNL), UT-Battelle, LLC, Climate Change Science Institute [Oak Ridge] (CCSI), UT-Battelle, LLC-UT-Battelle, LLC, Géosciences Paris Sud (GEOPS), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), MFRDC, 6 rue de la Perche 44700 Orvault, France, Department of Physical Geography and Quaternary Geology, Stockholm University, Division of Hydrologic Sciences, Desert Research Institute (DRI), Structure et fonctionnement des systèmes hydriques continentaux (SISYPHE), Université Pierre et Marie Curie - Paris 6 (UPMC)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Mines Paris - PSL (École nationale supérieure des mines de Paris), Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Golder Associates Kapellgränd 7, 11625 Stockholm, Sweden, Laboratoire d'Etudes Thermiques des Réacteurs (LETR), Département de Modélisation des Systèmes et Structures (DM2S), CEA-Direction des Energies (ex-Direction de l'Energie Nucléaire) (CEA-DES (ex-DEN)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-CEA-Direction des Energies (ex-Direction de l'Energie Nucléaire) (CEA-DES (ex-DEN)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Centre dor Water Resources Studies [Halifax] (CWRS), Dalhousie University [Halifax], Department of Civil and Resource Engineering [Halifax], Department of Earth and Planetary Sciences [Montréal] (EPS), McGill University = Université McGill [Montréal, Canada], Université Laval [Québec] (ULaval), Géosciences Environnement Toulouse (GET), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Laboratoire de biologie et modélisation de la cellule (LBMC UMR 5239), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre de Géosciences (GEOSCIENCES), Mines Paris - PSL (École nationale supérieure des mines de Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Technische Universität Darmstadt - Technical University of Darmstadt (TU Darmstadt), British Geological Survey (BGS), Swedish Nuclear Fuel and Waste Management Company, United States Geological Survey [Reston] (USGS), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Université Pierre et Marie Curie - Paris 6 (UPMC)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-MINES ParisTech - École nationale supérieure des mines de Paris, Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), MINES ParisTech - École nationale supérieure des mines de Paris, and TU Darmstadt Graduate School of Excellence Energy Science & Engineering

Subjects
010504 meteorology & atmospheric sciences, Groundwater flow, Discretization, 0208 environmental biotechnology, [SDU.STU]Sciences of the Universe [physics]/Earth Sciences, Permafrost, 02 engineering and technology, Numerical simulation, Hydrology and Quantitative Water Management, 01 natural sciences, Sharp interface problems, Range (statistics), ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences, Water Science and Technology, WIMEK, Computer simulation, Thermo-hydrological coupling, Mechanics, 020801 environmental engineering, Test case, Code benchmarking, 13. Climate action, [SDU]Sciences of the Universe [physics], Environmental science, Temporal discretization, Groundwater, Hydrologie en Kwantitatief Waterbeheer
Abstract

In high-elevation, boreal and arctic regions, hydrological processes and associated water bodies can be strongly influenced by the distribution of permafrost. Recent field and modeling studies indicate that a fully-coupled multidimensional thermo-hydraulic approach is required to accurately model the evolution of these permafrost-impacted landscapes and groundwater systems. However, the relatively new and complex numerical codes being developed for coupled non-linear freeze-thaw systems require verification. This issue is addressed by means of an intercomparison of thirteen numerical codes for two-dimensional test cases with several performance metrics (PMs). These codes comprise a wide range of numerical approaches, spatial and temporal discretization strategies, and computational efficiencies. Results suggest that the codes provide robust results for the test cases considered and that minor discrepancies are explained by computational precision. However, larger discrepancies are observed for some PMs resulting from differences in the governing equations, discretization issues, or in the freezing curve used by some codes.

Published
2018
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8. Upscaling of transport processes in porous media with biofilms in non-equilibrium conditions

Author

Michel Buès, Fabrice Golfier, Michel Quintard, Laurent Orgogozo, Laboratoire Environnement Géomécanique et Ouvrages (LAEGO), Institut National Polytechnique de Lorraine (INPL), Institut de mécanique des fluides de Toulouse (IMFT), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées, and ANR-10-BLAN-0908,MOBIOPOR,Modélisation de la biodégradation de polluants en milieu poreux: de la bactérie à l'échelle du terrain(2010)

Subjects
upscaling, Work (thermodynamics), [PHYS.MPHY]Physics [physics]/Mathematical Physics [math-ph], Porous media, 0207 environmental engineering, Direct numerical simulation, Reactive transport, 02 engineering and technology, Péclet number, 01 natural sciences, biofilm, [SPI.MECA.MEFL]Engineering Sciences [physics]/Mechanics [physics.med-ph]/Fluids mechanics [physics.class-ph], 010305 fluids & plasmas, Chemical kinetics, symbols.namesake, Phase (matter), Mass transfer, 0103 physical sciences, [SDU.STU.HY]Sciences of the Universe [physics]/Earth Sciences/Hydrology, 020701 environmental engineering, Water Science and Technology, Hydrology, [SDE.IE]Environmental Sciences/Environmental Engineering, Chemistry, Mechanics, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, Damköhler numbers, non-equilibrium, Biodegradation, symbols, Porous medium
Abstract

International audience; In this work, we derive two different Darcy-scale models for the transport of biodegradable solutes in porous media containing a microbial biomass that developed under the form of a biofilm. Biofilms are composed of bacterial populations and extra cellular polymeric substances, and grow attached to a solid-fluid interface, e.g. the pore walls of a water-saturated porous medium. We begin with the pore-scale description of mass transport, mass transfer between phases (fluid phase-generally water-and biofilm phase) and biologically-mediated reactions. Then, two limit cases of non-equilibrium transport are identified and characterized. Finally, these processes are upscaled using the method of volume averaging to obtain two different macroscale mass balance models. The models are derived for specific cases of non-equilibrium reactive transport (i.e., spatial concentration gradients may exist in one or both phases), for which mechanisms of mass transfer or reaction kinetics limit the rate of biodegradation. In both cases, a one-equation model can be developed even if non-equilibrium conditions exist. The validity domains of the two considered transport models (the Reaction-Rate Limited Consumption model-RRLC model-and the Mass Transfer Limited Consumption model-MTLC model) are established in terms of reactive and hydrodynamic conditions of transport (Damköhler number and Péclet number). The RRLC model is found to be consistent with direct numerical simulation (DNS) results at high Péclet and Damköhler numbers, while the applicability of the MTLC model is limited to high Damköhler numbers but low Péclet numbers.

Published
2010
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9. RichardsFoam2: A new version of RichardsFoam devoted to the modelling of the vadose zone

Author

Laurent Orgogozo, Géosciences Environnement Toulouse (GET), Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), and Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS)

Subjects
010504 meteorology & atmospheric sciences, Meteorology, Water flow, Computation, Rain, Scalar (mathematics), General Physics and Astronomy, Heterogeneous soils, 01 natural sciences, Evapotranspiration, Vadose zone, Applied mathematics, OpenFOAM®, Boundary value problem, [SDU.STU.AG]Sciences of the Universe [physics]/Earth Sciences/Applied geology, 0105 earth and related environmental sciences, [INFO.INFO-MS]Computer Science [cs]/Mathematical Software [cs.MS], Richards equation, 04 agricultural and veterinary sciences, Solver, Hardware and Architecture, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Geology
Abstract

International audience; RichardsFoam2 is an updated version of the OpenFOAM® solver RichardsFoam, presented in Orgogozo et al., Comput. Phys. Commun. 2014. The new features are the following: (i) The direct handling of fully heterogeneous porous media, with all the van Genuchten parameters defined as spatially varying scalar fields. (ii) The computation of the density of water flux at each face of the mesh cells, which allows the implementation of fixed water flux (e.g.: rain flux) boundary conditions. (iii) The integration in the water flow resolution of the actual evapotranspiration within the root zone, computed on the basis of the potential evapotranspiration. These new features allow to deal with the hydrology of real (i.e.: heterogeneous) soils in natural conditions, submitted to rain and evapotranspiration. Thus it considerably broadens the field of applicability of the OpenFOAM® solver for Richards equation. The description of the elements contained in this release may be found in the readMe file. In RichardsFoam2_presentation.pdf, one will find a more detailed description of the new features offered by RichardsFoam2 (equations, descriptions of the proposed test cases,…,…).

Published
2015
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10. Impact of biofilm-induced heterogeneities on solute transport in porous media

Author

Eric Lefevre, Tiangoua Kone, Laurent Orgogozo, Fabrice Golfier, J. C. Block, C. Oltean, Michel Buès, GeoRessources, Institut national des sciences de l'Univers (INSU - CNRS)-Centre de recherches sur la géologie des matières premières minérales et énergétiques (CREGU)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Université Nangui Abrogoua (UNA), Géosciences Environnement Toulouse (GET), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Laboratoire de Chimie Physique et Microbiologie pour l'Environnement (LCPME), Institut de Chimie du CNRS (INC)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Université Nangui Abrogoua, Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD), and Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)

Subjects
Materials science, biology, 0207 environmental engineering, Biofilm, Environmental engineering, [SDU.STU]Sciences of the Universe [physics]/Earth Sciences, 02 engineering and technology, 010501 environmental sciences, biology.organism_classification, 01 natural sciences, chemistry.chemical_compound, Brilliant Blue FCF, chemistry, Chemical engineering, Volume (thermodynamics), 13. Climate action, TRACER, Volume fraction, Shewanella oneidensis, 020701 environmental engineering, Porous medium, Porosity, 0105 earth and related environmental sciences, Water Science and Technology
Abstract

International audience; In subsurface systems, biofilm may degrade organic or organometallic pollutants contributing to natural attenuation and soil bioremediation techniques. This increase of microbial activity leads to change the hydrodynamic properties of aquifers. The purpose of this work was to investigate the influence of biofilm-induced heterogeneities on solute transport in porous media and more specifically on dispersivity. We pursued this goal by (i) monitoring both spatial concentration fields and solute breakthrough curves from conservative tracer experiments in a biofilm-supporting porous medium, (ii) characterizing in situ the changes in biovolume and visualizing the dynamics of the biological material at the mesoscale. A series of experiments was carried out in a flow cell system (60 cm(3)) with a silica sand (Phi = 50-70 mesh) as solid carrier and Shewanella oneidensis MR-1 as bacterial strain. Biofilm growth was monitored by image acquisition with a digital camera. The biofilm volume fraction was estimated through tracer experiments with the Blue Dextran macromolecule as in size-exclusion chromatography, leading to a fair picture of the biocolonization within the flow cell. Biofilm growth was achieved in the whole flow cell in 29 days and up to 50% of void space volume was plugged. The influence of biofilm maturation on porous medium transport properties was evaluated from tracer experiments using Brilliant Blue FCF. An experimental correlation was found between effective (i.e., nonbiocolonized) porosity and biofilm-affected dispersivity. Comparison with values given by the theoretical model of Taylor and Jaffe (1990b) yields a fair agreement.

Published
2014
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11. An open source massively parallel solver for Richards equation: Mechanistic modelling of water fluxes at the watershed scale

Author

Sat Kumar Tomer, Florent Henon, Laurent Orgogozo, Muddu Sekhar, Oleg S. Pokrovsky, Cyprien Soulaine, Nicolas Renon, Rachid Ababou, David Labat, Michel Quintard, Géosciences Environnement Toulouse (GET), Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD), Calcul en Midi-Pyrénées (CALMIP), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-PRES Université de Toulouse, Institut de mécanique des fluides de Toulouse (IMFT), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées, Centre d'études spatiales de la biosphère (CESBIO), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS), Tomsk State University [Tomsk], Indo-French Cell for Water Sciences (IFCWS), Indian Institute of Science [Bangalore] (IISc Bangalore), Centre National d'Études Spatiales - CNES (FRANCE), Centre National de la Recherche Scientifique - CNRS (FRANCE), Indian Institute of Science - IISC (INDIA), Institut National Polytechnique de Toulouse - INPT (FRANCE), Institut de Recherche pour le Développement - IRD (FRANCE), Université Toulouse III - Paul Sabatier - UT3 (FRANCE), Tomsk State University - TSU (RUSSIA), Institut de Mécanique des Fluides de Toulouse - IMFT (Toulouse, France), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Calcul en Midi-Pyrénée (CALMIP), Université de Toulouse (UT)-Université de Toulouse (UT)-PRES Université de Toulouse-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Томский государственный университет Институт биологии, экологии, почвоведения, сельского и лесного хозяйства (Биологический институт) Научные подразделения БИ, Institut National Polytechnique de Toulouse - Toulouse INP (FRANCE), Météo-France -Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Université Fédérale Toulouse Midi-Pyrénées-Centre National d'Études Spatiales [Toulouse] (CNES)-Météo-France -Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES), Centre National de la Recherche Scientifique (CNRS)-PRES Université de Toulouse-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), and Météo-France -Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Université Fédérale Toulouse Midi-Pyrénées-Centre National d'Études Spatiales [Toulouse] (CNES)-Météo-France -Centre National de la Recherche Scientifique (CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)

Subjects
FOS: Computer and information sciences, Source code, 010504 meteorology & atmospheric sciences, Computer science, Hydraulic engineering, media_common.quotation_subject, Mécanique des fluides, [PHYS.MPHY]Physics [physics]/Mathematical Physics [math-ph], 0207 environmental engineering, Porous media, General Physics and Astronomy, 02 engineering and technology, Computational fluid dynamics, 01 natural sciences, водные потоки, Civil Engineering, Computational science, Computational Engineering, Finance, and Science (cs.CE), OpenFOAM®, [SDU.STU.HY]Sciences of the Universe [physics]/Earth Sciences/Hydrology, Computer Science - Computational Engineering, Finance, and Science, 020701 environmental engineering, Scaling, Massively parallel, 0105 earth and related environmental sciences, media_common, механическое моделирование, business.industry, [SDE.IE]Environmental Sciences/Environmental Engineering, Ричардса уравнение, Richards equation, водные бассейны, Solver, Variably saturated flow, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Water resources, Computer Science - Distributed, Parallel, and Cluster Computing, Hardware and Architecture, Distributed, Parallel, and Cluster Computing (cs.DC), Massively parallel computation, [INFO.INFO-DC]Computer Science [cs]/Distributed, Parallel, and Cluster Computing [cs.DC], business, Transfers in soils
Abstract

In this paper we present a massively parallel open source solver for Richards equation, named the RichardsFOAM solver. This solver has been developed in the framework of the open source generalist computational fluid dynamics tool box OpenFOAM (R) and is capable to deal with large scale problems in both space and time. The source code for RichardsFOAM may be downloaded from the CPC program library website. It exhibits good parallel performances (up to similar to 90% parallel efficiency with 1024 processors both in strong and weak scaling), and the conditions required for obtaining such performances are analysed and discussed. These performances enable the mechanistic modelling of water fluxes at the scale of experimental watersheds (up to few square kilometres of surface area), and on time scales of decades to a century. Such a solver can be useful in various applications, such as environmental engineering for long term transport of pollutants in soils, water engineering for assessing the impact of land settlement on water resources, or in the study of weathering processes on the watersheds. (C) 2014 Elsevier B.V. All rights reserved.

Published
2014
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12. Biofilms in porous media: development of macroscopic transport equations via volume averaging with closure for local mass equilibrium conditions

Author

Michel Quintard, Brian D. Wood, Laurent Orgogozo, Michel Buès, Fabrice Golfier, Centre National de la Recherche Scientifique - CNRS (FRANCE), Institut National Polytechnique de Lorraine - INPL (FRANCE), Institut National Polytechnique de Toulouse - Toulouse INP (FRANCE), Université Toulouse III - Paul Sabatier - UT3 (FRANCE), Oregon State University (USA), Université Henri Poincaré-Nancy1 - UHP (FRANCE), and Institut de Mécanique des Fluides de Toulouse - IMFT (Toulouse, France)

Subjects
Physics, Ecologie, Environnement, Work (thermodynamics), Homogenization, 010504 meteorology & atmospheric sciences, Mass balance, Biofilm, 0207 environmental engineering, Thermodynamics, 02 engineering and technology, Mechanics, Dispersion, 01 natural sciences, Homogenization (chemistry), Domain (mathematical analysis), Local mass equilibrium, Averaging, Mass transfer, Tensor, 020701 environmental engineering, Porous medium, Dispersion (water waves), 0105 earth and related environmental sciences, Water Science and Technology
Abstract

In this work, we upscale a pore-scale description of mass transport in a porous medium containing biofilm to develop the relevant Darcy-scale equations. We begin with the pore-scale descriptions of mass transport, interphase mass transfer, and biologically-mediated reactions; these processes are then upscaled using the method of volume averaging to obtain the macroscale mass balance equations. We focus on the case of local mass equilibrium conditions where the averaged concentrations in the fluid and biological phases can be assumed to be proportional and for which a one-equation macroscopic model may be developed. We predict the effective dispersion tensor by a closure scheme that is solved for the cases of both simple and complex unit cells. The domain of validity of the approach is clearly identified, both theoretically and numerically, and unitless groupings indicating the domain of validity are reported.

Published
2009

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