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Last update: May 2021

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Virtual soil project

Welcome to the VSoil project!

VSoil is a modelling software platform supported by the "Agroécosystèmes" division of INRAE and developed and hosted by EMMAH laboratory. It is a tool to help develop numerical models describing the physical, chemical and biological processes of the soil in interaction with the climate, plants and anthropic actions. By facilitating the coupling between these processes, the platform makes it possible to develop complex models from assemblies of existing or new codes.

You can find below all the news about the VSoil project: new stable versions of VSoil software suite, new collaborations (projects, thesis, ...), ...

Look also at the left of this page to access more informations about the VSoil project: description of the project and the software platform, informations about the project life, procedures to download the VSoil software suite (on Linux and Windows), access to documentations of the VSoil software suite (including some tutorials) and how to contact us.

News

  • Mostafa Moradzadeh (INRAE, EMMAH, Avignon) joined the VSoil project as a new modeler. He works on the VSoilForOAD project since April 2022 until the end of December 2022 in replacement of Manon Martin who found a new job. Mostafa more precisely carries out some sensitivity analysis in order to identify the relative influence of some parameters of the model developed in this project (climatic, soil, vegetation, phenological and mulch parameters, and boundary conditions) on a set of model outputs produced by the module implementing the "soil praticability" process (saturation index, praticability index and drying slope). To do that, two methods implementing the Monte Carlo estimation of the Sobol' indices, named soboljansen and sobolSalt (from "sensitivity" R package), were added in the list of R sensitivity analysis methods available in VSoil. 25/08/2022
  • Julien Ardouin (Savoie Mont Blanc University) joined the VSoil project as a new modeler during his master internship (February - August 2022) for a topic entitled "Sensitivity analysis and inversion of a coupled hydro-geophysical model". This internship is the continuation of the work started by Ismaïl Djellouli (see below). Julien improved the module implementing the "petrophysics" process by adding an option allowing to correct the true resistivity by the temperaure provided by a module solving the heat transport equation. Julien then used the Morris sensitivity analysis method available in the VSoil platform to estimate the relative importance of hydraulic and geophysics parameters on electrical apparent resisitivity and water volumetric content values. Julien also used and improved the SCE-UA optimization algorithm available in the VSoil platform to infer hydraulic and geophysics parameters from reference or measured values of electrical apparent resistivitiy and water volumetric content. Julien launched his simulations on the Linux VSoil calculation server available in EMMAH (INRAE, Avignon). At least, Julien developed a Python script allowing to create easily the files (electrical mesh and configuration of electrodes) to be read by the module implementing the "electrical transport" process. 18/08/2022
  • A new stable version of VSoil software suite (VSoil 20220810) is available. The main features introduced in this version are: (1) make official several processes, modules and models, (2) module parameters can be conditionally disabled, depending on the values of other parameters, (3) replace subroutine_succedeed variable by stop_simulation in "initialization", "compute", "interpolate outputs", "validate" and "end" sections of modules, (4) add a tool allowing to identify graphically differences between outputs of models, (5) add the Sobol sensitivity method, (6) add a free section to add the R source code of the user. See the Technical news page for more details about this version and the Download page to download and install it. 10/08/2022
  • A presentation and a demonstration of the VSoil platform and of the model being developed as part of the VSoilForOAD project took place in Avignon on 4 May 2022. 5 persons participated in this day coming from INRAE and ONF. 04/05/2022
  • Manon Martin recently developed several modules that have been integrated to the model she is developing for the VSoilForOAD project: (1) a C++ module that implements the "climate" process and reads climatic data from different sources: SAFRAN, Météo-France or local data, (2) a C++ module that implements the "evapotranspiration" process and has the capacity to read hourly PET (potential evapotranspiration) data or calculate PET values from climatic data using the ASCE standardized Penman-Monteith formulation, (3) a Fortran module that implements the "crop development" process and calculates a leaf area index profile (using read or calculated phenological dates) and root lengths, and (4) a C++ module that implements the new created "soil praticability" process and that calculates several soil saturation and soil praticability indexes. Moreover, the Sobol sensitivity analysis method (from "sensitivity" R package) was added in the list of R sensitivity analysis methods available in VSoil in order Manon can run sensitivity analysis with experimental design built with both continuous and discrete parameters (an example of discrete parameter is the origin of climatic data: SAFRAN, Météo-France or local). 03/05/2022
  • Enzo Dos Santos joined the VSoil project from 28/03/2022 to 19/06/2022 as part of a second year internship at the University Institute of Technology in Computer Science in Aix-Marseille. The subject of his internship is: "Implementation of a database for the VSoil project models inventory". As the number of modules and models within the VSoil project grew, it became important to implement a mechanism to enable their inventory. Enzo will work on the following tasks: (1) Collect information on modules and models from several sources. (2) Complement these sources with additional, more volatileinformation. (3) Format and present the relevant information online on the project website. (4) Add filters and search functions. 28/03/2022
  • A new stable version of VSoil software suite (VSoil 20220127) is available. The main features introduced in this version are: (1) make official several models and modules, (2) replace subroutine_succedeed variable by reduce_dt in compute section of modules, (3) modules can now use external libraries Blas and Lapack on Windows, (4) introduce "stop and resume" capability for models, (5) add SCE-UA and DreamZS parameter optimization methods, (6) enable parallel run for Morris method (sensitivity analysis). See the Technical news page for more details about this version and the Download page to download and install it. 27/01/2022
  • Hamza Chaif (INRAE, EMMAH, Avignon) joined the VSoil Project as a new modeler. He started his post-doctorate in September 2021 as part of the SmartFertiReuse project. In order to model the transfer in the soil of contaminants present in the treated wastewater, Hamza uses a 1D mechanistic soil transfer model based on the PASTIS model and implemented in the VSoil platform. Both pedotransfer functions and colloids retention parameters need to be determined. To do so, the DREAMzs bayesian parameter estimation method was added in the list of R parameter estimation methods available in VSoil. More details on Hamza's work here. 14/12/2021
  • Manon Martin (INRAE, EMMAH, Avignon) started a new collaboration with the VSoil project. She started her post-doctorate in January 2020 as part of the VSoilForOAD project which aims to develop a prototype of a climate service capable of predicting the practicability of the traffic routesfor logging machinery. For this, she uses a 1D mechanistic soil transfer model based on the PASTIS model, implemented in the VSoil platform and adapted to the forestry context. The objective of Manon is to simplify the parameterisation of this model and to use easily accessible data. For this purpose, Manon created a VSoil module implementing several pedotransfer functions to identify the one that is most adapted to forest soils and she will use the Fast99 sensitivity analysis method available in VSoil to evaluate the key parameters for predicting water dynamics of forest soils. A new feature is being developed by the VSoil team to stop and resume a simulation in order Manon can use VSoil to provide real-time water dynamics. More details on Manon's work here. 17/11/2021
  • Elisabeth Fries (Gustave Eiffel University, Champs-sur-Marne) joined the VSoil project as a new modeler. She started in January 2021 her PhD thesis entitled "Transport and retention of fluorinated pollutants in soils: small scale experiments, magnetic resonance imaging and computer simulations". Elisabeth started using the official CDE_column model from VSoil platform to simulate the transport of fluorinated pollutants in a soil column. During her PhD she will improve this model by taking into account different mechanisms of adsorption of these pollutants onto soil. To calibrate some parameters of the model, she will use the Levenberg-Marquardt's and DREAM optimisation algorithms available in VSoil. More details on Elisabeth's work here. 30/07/2021
  • Ismaïl Djellouli (Sorbonne University, Paris) joined the VSoil project as a new modeler. He used the VSoil platform during his master internship (March - August 2021) for a topic entitled "Inversion of soil hydraulic properties with a coupled modelling of soil water transfers and electrical resistivity tomography survey". He added in VSoil two processes named "petrophysics" and "electrical transport" and two C++ modules implementing these processes. The module implementing the "electrical transport" process used Gimli, a library for geophysical modelling and inversion. In order to estimate hydraulic and petrophysical parameters, the SCE-UA optimization algorithm was added in the list of R parameter estimation methods available in VSoil. The Morris sensitivity analysis method available in VSoil was previously used to determine the least sensitive parameters which are thus fixed in the parameter estimation. More details on Ismaïl's work here. 20/07/2021
  • A new stable version of VSoil software suite (VSoil 20210527) is available. The main features introduced in this version are: (1) make official several models and modules, (2) make official a C++ module running a Python script with an embedded Python interpreter), (3) add the possibility to duplicate inputs/outputs, (4) add physical subroutines to be used in Fortran modules, (5) add an utility function calculating the 1D integral of the product of two functions (Fortran only). See the Technical news page for more details about this version and the Download page to download and install it. 27/05/2021
  • A new stable version of VSoil software suite (VSoil 20210115) is available. The main features introduced in this version are: (1) make official several models and modules, (2) improve API on exported models, (3) introduce an external diff tool (Linux only) to compare modules source codes, (4) add 3 biological functions (Andren, q10 and Vanthoff) available from modules (Fortran only), (5) allow iterations between modules when they are strongly coupled by their inputs/outputs. See the Technical news page for more details about this version and the Download page to download and install it. 15/01/2021
  • Nicolas Beudez (INRAE, EMMAH, Avignon) joined the laboratory and the VSoil project as a permanent member. He left AMAP laboratory (Montpellier) within the scope of an internal INRAE mobility. He is a scientific computing engineer and will take over part of the activities of the current scientific manager of the VSoil project (François Lafolie, INRAE, EMMAH) who will soon retire. 01/10/2020
  • A new stable version of VSoil software suite (VSoil 20200907) is available. The main features introduced in this version are: make official several models and modules. See the Technical news page for more details about this version and the Download page to download and install it. 07/09/2020
  • A new stable version of VSoil software suite (VSoil 20200609) is available. The main features introduced in this version are: (1) make official several models, modules and processes, (2) new remote connection to Meso@LR cluster in Montpellier, (3) add a template for module user documentation. See the Technical news page for more details about this version and the Download page to download and install it. 09/06/2020
  • A new stable version of VSoil software suite (VSoil 20200330) is available. The main features introduced in this version are: (1) make official several modules, (2) update some modules to manage grid change (interpolate of profile outputs), (3) new save frequency "after nb iterations" replaces "save each validate", (4) improve runtime performance of some modules and vsoil utility functions, (5) new CPU management for parallel run to improve multiple concurrent jobs on the same computer. See the Technical news page for more details about this version and the Download page to download and install it. 30/03/2020
  • A new stable version of VSoil software suite (VSoil 20200113) is available. The main features introduced in this version are: (1) make official several models, modules and processes, (2) general filter is now usable, (3) allow save frequency in years, (4) add batch (multi-run) capabilty. See the Technical news page for more details about this version and the Download page to download and install it. 13/01/2020
  • Manon Martin (Avignon University) will defend her PhD entitled "Development of a water balance model in forest soil partly compacted using parsimonious data" on 16 October 2019. You can find here an abstract (in french and in english) of this thesis. 14/10/2019

Previous news

Landmarks 2013 :

  • Launch of version 1.0 of the virtual soil platform 1rst March 2013. The plateform is now complete with its 4 softwares, from processes definition to model usage. (Click here to download)

Previous landmarks :

  • November 2012: Training to the complete Vsoil platform.

The aim is to train new platform users and to favour the exchanges between them.

  • The platform is a partner of two scientific projects of the Environment and Agronomy Department. The platform is also involved in the AnaEE-France project. See the AnaEE web site for details. (www.anaee-s.fr)
  • Two training sessions have been organized in 2011.
  • During summer 2011 : a summer practical training for automation of tests for the graphical user interfaces. Its is a first step towards the setting up of a continuous integration platform.
  • August 2010. An engineer joined the development team. September 2010 a student in alternating training (BTS level) joined the team.
  • July 2010 : A document describing the technical choices is released. This document is based on the analysis document and prepares the detailed conception document.
  • November 2009: An analysis document is released. It is based on the functionnal specifications given by the Management Group in charge of platform development overseing.
  • January 2009 : The Environmment and Agronomy Department of INRA launches the Vsoil platform project. It defines the organisation of the project.
  • February 2008 The E&A department sets up a group of scientists with various thematic fields to define the functionnal specifications of the platform. The group visited most of the laboratories and the document containing the functionnal specifications was available by the end of October 2008.
  • November 2006 The deparrment sets up four reflexion groups with different thematic fields.
  • April 2006 The Environment and Agronomy Department initiates the idea of setting up a modeling platform. Its aims are : to promote the development of models for the simulation of the various processes occuring in the soil and at the interfaces between the soil and the atmosphere ; to promote the re-use of models and modules developped ; to promote the collaboration between scientists of various thematic fields ; to promote the collaboration between specialists of the modelling and specialists of observations.

News

All news

PhD-defense Flavien Poincot

Flavien Poincot (Université Orléans) will defend his PhD entitled “Effect of soil structural conditions on nitrous oxide emissions” April 5,2019.
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PhD-defense Laurent BLEUZE

Laurent Bleuze (Université Champagne Ardennes) defended his PhD thesis : "Dew retting of industrial hemp(Cannabis sativa L.): dynamics under...
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PhD-defense Anne-Sophie Lissy

Anne-Sophie Lissy (Avignon University) defended its thesis on February 7, 2019.
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PhD-defense Manon Martin

Manon MARTIN (AVIGNON Université) will defend her PhD entitled "Development of a water balance model in forest soil partly compacted using...
Read more

See all news