Softwares
eLYSe | Kesaco | NaSCar | NS-MPI-2D-3D | Others
eLYSe
Participants: Olivier Saut [correspondant], Raphael Bahegne, Vincent Hubert, Jean-Baptiste Lagaert, Mathieu Specklin.
eLYse is a numerical platform used for our computations in Biology (tumor growth), micro-fluidics and complex Newtonian fluid flows. The platform is divided in two libraries : one is devoted to the modelling equations and the other one includes the numerical solvers. For example, we are able to treat (in 2D and 3D) transport equations, diffusion equations, Navier-Stokes equations, Maxwell system and the interaction fluid-structure by level-set and penalization methods. The solvers are based on finite volume methods on cartesian grids and allow parallel computations. See also the web page http://www.math.u-bordeaux1.fr/~saut/wp/?page_id=201.
- Version: 0.4
- ACM: ACM J.2 J.3 G.1.8 G.1.10
- AMS: AMS65Z05 35Q92
- Keywords: Modélization and numerical simulations, Finite volume methods, Level Set approach, Penalization method
- APP: En cours
- Type of human computer interaction: console
- OS/Middelware: Platform developped on Mac OS X architecture.
- Required library or software: Petsc (http://www.mcs.anl.gov/petsc/petsc-as/)Vtk (http://www.vtk. org/)Blitz++ (http://www.oonumerics.org/blitz/) (optionnel)Boost (http://www.boost.org/)
- Programming language: C++
- Documentation: doxygen.
Kesaco
Participants: Olivier Saut [correspondant], Raphaël Bahègne, Damiano Lombardi, Mathieu Specklin.
Kesaco is a set of libraries and programs aiming at applications of mathematical modeling in clinical oncology. It features:
- A library of specialized mathematical model describing the growth of different types of cancers (secondary tumors in the lung, gliomas).
- A set of programs useful to validate mathematical models (compute the various behavior they can produce) and to build databases of numerical simulations.
- Segmentation and registration routines to use medical images directly in our numerical codes.
- Calibration methods to recover the parameters of the models using sequences of medical images. Three techniques are implemented (a genetic algorithm, a technique based on reduced order models, a sensitivity technique).
All these routines are adapted to run on a MP architecture. The webpage may be found at http://www.math.ubordeaux1.fr/~saut/wp/?page_id=345.
- Version: 0.1
- Keywords: Modélization and numerical simulations
- APP: En cours
- Type of human computer interaction: console
- OS/Middelware: Platform developped on Mac OS X architecture.
- Required library or software: eLYSe, Insight Toolkit (http://www.itk.org)
- Programming language: C++
- Documentation: doxygen.
NaSCar
Participant: Michel Bergmann [correspondant].
Participants: Olivier Saut [correspondant], Raphael Bahegne, Vincent Hubert, Jean-Baptiste Lagaert, Mathieu Specklin.
eLYse is a numerical platform used for our computations in Biology (tumor growth), micro-fluidics and complex Newtonian fluid flows. The platform is divided in two libraries : one is devoted to the modelling equations and the other one includes the numerical solvers. For example, we are able to treat (in 2D and 3D) transport equations, diffusion equations, Navier-Stokes equations, Maxwell system and the interaction fluid-structure by level-set and penalization methods. The solvers are based on finite volume methods on cartesian grids and allow parallel computations. See also the web page http://www.math.u-bordeaux1.fr/~saut/wp/?page_id=201.
- Version: 0.4
- ACM: ACM J.2 J.3 G.1.8 G.1.10
- AMS: AMS65Z05 35Q92
- Keywords: Modélization and numerical simulations, Finite volume methods, Level Set approach, Penalization method
- APP: En cours
- Type of human computer interaction: console
- OS/Middelware: Platform developped on Mac OS X architecture.
- Required library or software: Petsc (http://www.mcs.anl.gov/petsc/petsc-as/)Vtk (http://www.vtk. org/)Blitz++ (http://www.oonumerics.org/blitz/) (optionnel)Boost (http://www.boost.org/)
- Programming language: C++
- Documentation: doxygen.
Kesaco
Participants: Olivier Saut [correspondant], Raphaël Bahègne, Damiano Lombardi, Mathieu Specklin.
Kesaco is a set of libraries and programs aiming at applications of mathematical modeling in clinical oncology. It features:
- A library of specialized mathematical model describing the growth of different types of cancers (secondary tumors in the lung, gliomas).
- A set of programs useful to validate mathematical models (compute the various behavior they can produce) and to build databases of numerical simulations.
- Segmentation and registration routines to use medical images directly in our numerical codes.
- Calibration methods to recover the parameters of the models using sequences of medical images. Three techniques are implemented (a genetic algorithm, a technique based on reduced order models, a sensitivity technique).
All these routines are adapted to run on a MP architecture. The webpage may be found at http://www.math.ubordeaux1.fr/~saut/wp/?page_id=345.
- Version: 0.1
- Keywords: Modélization and numerical simulations
- APP: En cours
- Type of human computer interaction: console
- OS/Middelware: Platform developped on Mac OS X architecture.
- Required library or software: eLYSe, Insight Toolkit (http://www.itk.org)
- Programming language: C++
- Documentation: doxygen.
NaSCar
Participant: Michel Bergmann [correspondant].
This code is devoted
to solve 3D-flows in around moving and deformable
bodies. The incompressible Navier- Stokes
equations are solved on fixed grids, and the
bodies are taken into account thanks to
penalization and/or immersed boundary methods. The
interface between the fluid and the bodies is
tracked with a level set function or in a
Lagrangian way. The numerical code is fully second
order (time and space). The numerical method is
based on projection schemes of Chorin-Temam’s
type. The code is written in C language and
use Petsc (http://www.mcs.anl.gov/petsc/petsc-as/)
library for the resolution of large linear systems
in parallel. NaSCar can be used to simulate both
hydrodynamic bio-locomation as fish like swimming
and aerodynamic flows such wake generated by a wind
turbine.
- Version: 1
- Keywords: numerical analyse, fluid mechanics, langage C, PETSc
- Software benefit : simulate a flow around a deformable obstacle, moving into a fluid.
- APP: En cours
- Patent: non
- Type of human computer interaction: human for the moment
- OS/Middelware: unix, linux, mac os
- Required library or software: PETSc
- Programming language: C
- Documentation: in progess
NS-MPI-2D-3D
Participant: Charles-Henri Bruneau [correspondant], K. Khadra and Yong Liang Xiong
The software NS-MPI-2D-3D is a numerical platform devoted to the computation of the incompressible flow around bodies in two or three dimensions modelled by Stokes, Navier-Stokes or Oldroyd-B equations. It is based on finite differences or finite volumes approximations on cartesian grid using the volume penalization method to handle the obstacles. It is written using Fortran 95 programming language and is fully parallelized with MPI procedures to run on hundreds of cores.
This software is the property of Ch-H bruneau. K. Khadra has participated to MPI parallelism and Yong Liang Xiong to the extension to Oldroyd-B model.
Other MC2 codes
- Version: 1
- Keywords: numerical analyse, fluid mechanics, langage C, PETSc
- Software benefit : simulate a flow around a deformable obstacle, moving into a fluid.
- APP: En cours
- Patent: non
- Type of human computer interaction: human for the moment
- OS/Middelware: unix, linux, mac os
- Required library or software: PETSc
- Programming language: C
- Documentation: in progess
NS-MPI-2D-3D
Participant: Charles-Henri Bruneau [correspondant], K. Khadra and Yong Liang Xiong
The software NS-MPI-2D-3D is a numerical platform devoted to the computation of the incompressible flow around bodies in two or three dimensions modelled by Stokes, Navier-Stokes or Oldroyd-B equations. It is based on finite differences or finite volumes approximations on cartesian grid using the volume penalization method to handle the obstacles. It is written using Fortran 95 programming language and is fully parallelized with MPI procedures to run on hundreds of cores.
This software is the property of Ch-H bruneau. K. Khadra has participated to MPI parallelism and Yong Liang Xiong to the extension to Oldroyd-B model.
Other MC2 codes
- Vortex:
sequential, Vortex In-Cell (VIC) scheme : hybrid
vortex methods based on the combination of
Lagrangian mesh-free schemes and Eulerian grid
based schemes on the same flow region.
- Unstructured body fitted meshes
- Richards : 2D Unstructured finite element code, implicit solver, sequential, to solve the transport-diffusion equations through a porous media including tidal forcing and mechanisms of diagenesis.
- Compressible flows and elliptic problems
- Compressible flows : 2D-3D finite volume scheme pour compressible Euler/NS equations on cartesian grids
- Elliptic problems : 2D-3D finite difference scheme for elliptic interface problems, sequential and parallel
- Unstructured body fitted meshes
- Richards : 2D Unstructured finite element code, implicit solver, sequential, to solve the transport-diffusion equations through a porous media including tidal forcing and mechanisms of diagenesis.
- Compressible flows and elliptic problems
- Compressible flows : 2D-3D finite volume scheme pour compressible Euler/NS equations on cartesian grids
- Elliptic problems : 2D-3D finite difference scheme for elliptic interface problems, sequential and parallel
