https://www.coria-cfd.fr/api.php?action=feedcontributions&feedformat=atom&user=Pmatteoli 2026-05-11T22:33:12Z User contributions MediaWiki 1.26.2 https://www.coria-cfd.fr/index.php?title=YALES2BIO&diff=4193 2020-07-20T12:00:02Z

<p>Pmatteoli: /* Private wiki */</p> <hr /> <div>{{#customtitle:YALES2BIO public page|YALES2BIO public page - www.coria-cfd.fr}}<br /> == Motivation ==<br /> <br /> YALES2BIO aims at solving the equations of fluid dynamics in the context of biological flows. The main application is cardiovoscular flows, involving microscale (at the level of cells) and macro-scale applications (blood flow in the heart).<br /> <br /> YALES2BIO was developed from 2010 to 2013 by [[User:Mendez|S. Mendez]] and [[User:Chnafa|C. Chnafa]] and is maintained since 2012 by [[User:Mendez|S. Mendez]] at I3M, together with the YALES2 developers at CORIA.<br /> <br /> == Solvers ==<br /> <br /> YALES2BIO is based on [[YALES2|YALES2]]. In addition to the solvers implemented in YALES2, YALES2BIO has several specific solvers.<br /> * Red blood cell solver ('''RBC''')<br /> * Electrostatics solver ('''ESS''')<br /> * ALE solver, with specific routines for heart ('''ALE''')<br /> <br /> All the following features are inherited from the YALES2 kernel:<br /> <br /> == Models ==<br /> * Turbulence (Large-Eddy Simulation)<br /> ** Constant Smagorinsky<br /> ** Localized dynamic Smagorinsky<br /> ** WALE<br /> ** SIGMA<br /> <br /> == Numerics ==<br /> * Spatial: 2nd- and 4th-order finite-volume schemes<br /> * Temporal:<br /> ** 4th-order explicit time integration (RK4 and TFV4A) of convective terms<br /> ** explicit and implicit diffusion and source terms<br /> * Stabilization: Cook &amp; Cabot 4th-order artificial viscosity<br /> * Linear solvers:<br /> ** PCG<br /> ** BICGSTAB, BICGSTAB2, BICGSTAB(2)<br /> ** Deflated PCG<br /> ** Deflated BICGSTAB(2)<br /> ** Residual recycling<br /> <br /> == Data Structures ==<br /> * 1D, 2D, 3D unstructured solver<br /> * Full dual decomposition based on METIS<br /> * Data registration (int, real, char, node, elem, face, pair, scalar, vector, tensor)<br /> * Optimized non-blocking MPI communications<br /> * Parallel load balancing<br /> * Automatic reconnection of periodic boundaries<br /> * Automatic homogeneous mesh refinement<br /> * IO formats: Gambit (Fluent), Ensight, prepartionned HDF5 (XDMF) with compression<br /> * Cartesian mesh generator<br /> * Partitioned mesh support for HDF5 independent of the number of processors<br /> * Parallel interpolator for partitioned HDF5 meshes<br /> * Automatic sponge layers<br /> * Built-in Gaussian filters of arbitrary size<br /> <br /> == Software engineering ==<br /> * 185,000 lines of code<br /> * Object-oriented fortran with modules (f90)<br /> * Version management with GIT<br /> * Inline documentation in the source code (XML + Latex)<br /> * GUI with client/server mode (wxwidgets, C++)<br /> * Automatic validation tests (AQAT, AVVT)<br /> * Automatic dependency of f90 modules in makefiles<br /> * Keyword-based input file<br /> * Easy profiling with timers<br /> <br /> == Gallery ==<br /> Some computation examples are given in the [[YALES2_Gallery|gallery]] (Simulation of a cardiac cycle).<br /> <br /> == Private wiki ==<br /> To access the YALES2BIO private wiki, click on this link [https://yales2bio.coria-cfd.fr/index.php/Main_Page].</div>

Pmatteoli https://www.coria-cfd.fr/index.php?title=YALES2BIO&diff=4192 2020-07-20T11:57:38Z

<p>Pmatteoli: /* Gallery */</p> <hr /> <div>{{#customtitle:YALES2BIO public page|YALES2BIO public page - www.coria-cfd.fr}}<br /> == Motivation ==<br /> <br /> YALES2BIO aims at solving the equations of fluid dynamics in the context of biological flows. The main application is cardiovoscular flows, involving microscale (at the level of cells) and macro-scale applications (blood flow in the heart).<br /> <br /> YALES2BIO was developed from 2010 to 2013 by [[User:Mendez|S. Mendez]] and [[User:Chnafa|C. Chnafa]] and is maintained since 2012 by [[User:Mendez|S. Mendez]] at I3M, together with the YALES2 developers at CORIA.<br /> <br /> == Solvers ==<br /> <br /> YALES2BIO is based on [[YALES2|YALES2]]. In addition to the solvers implemented in YALES2, YALES2BIO has several specific solvers.<br /> * Red blood cell solver ('''RBC''')<br /> * Electrostatics solver ('''ESS''')<br /> * ALE solver, with specific routines for heart ('''ALE''')<br /> <br /> All the following features are inherited from the YALES2 kernel:<br /> <br /> == Models ==<br /> * Turbulence (Large-Eddy Simulation)<br /> ** Constant Smagorinsky<br /> ** Localized dynamic Smagorinsky<br /> ** WALE<br /> ** SIGMA<br /> <br /> == Numerics ==<br /> * Spatial: 2nd- and 4th-order finite-volume schemes<br /> * Temporal:<br /> ** 4th-order explicit time integration (RK4 and TFV4A) of convective terms<br /> ** explicit and implicit diffusion and source terms<br /> * Stabilization: Cook &amp; Cabot 4th-order artificial viscosity<br /> * Linear solvers:<br /> ** PCG<br /> ** BICGSTAB, BICGSTAB2, BICGSTAB(2)<br /> ** Deflated PCG<br /> ** Deflated BICGSTAB(2)<br /> ** Residual recycling<br /> <br /> == Data Structures ==<br /> * 1D, 2D, 3D unstructured solver<br /> * Full dual decomposition based on METIS<br /> * Data registration (int, real, char, node, elem, face, pair, scalar, vector, tensor)<br /> * Optimized non-blocking MPI communications<br /> * Parallel load balancing<br /> * Automatic reconnection of periodic boundaries<br /> * Automatic homogeneous mesh refinement<br /> * IO formats: Gambit (Fluent), Ensight, prepartionned HDF5 (XDMF) with compression<br /> * Cartesian mesh generator<br /> * Partitioned mesh support for HDF5 independent of the number of processors<br /> * Parallel interpolator for partitioned HDF5 meshes<br /> * Automatic sponge layers<br /> * Built-in Gaussian filters of arbitrary size<br /> <br /> == Software engineering ==<br /> * 185,000 lines of code<br /> * Object-oriented fortran with modules (f90)<br /> * Version management with GIT<br /> * Inline documentation in the source code (XML + Latex)<br /> * GUI with client/server mode (wxwidgets, C++)<br /> * Automatic validation tests (AQAT, AVVT)<br /> * Automatic dependency of f90 modules in makefiles<br /> * Keyword-based input file<br /> * Easy profiling with timers<br /> <br /> == Gallery ==<br /> Some computation examples are given in the [[YALES2_Gallery|gallery]] (Simulation of a cardiac cycle).<br /> <br /> == Private wiki ==<br /> To access the YALES2BIO private wiki, click here</div>

Pmatteoli