We consider a dual-mixed variational formulation of the Darcy-Forchheimer model. Assuming that the permeability is a symmetric and positive-definite tensor, we prove the problem is well-posed. For the discretization, we approximate the velocity-pressure pair by Raviart-Thomas elements of the lowest order and piecewise constants, respectively. The corresponding discrete problem is well-posed, and we derive a priori error estimates. We also develop an a posteriori error analysis of the residual type and show the reliability of the new a posteriori error indicator. Finally, we provide some numerical experiments that support the theoretical results and suggest the indicator’s eventual efficiency.

Abstract In this work, we consider a linearized model for fluid flow through a deformable porous elastic solid derived using mixture theory. The model accounts for small but non-negligible solid velocity relative to the fluid, resulting in a coupled system of equations. We focus on the error analysis and implementation of two fully discrete schemes: one using the first-order backward Euler method for time discretization and the other employing the second-order BDF2 scheme. We derive error estimates for both procedures and describe numerical experiments on the corresponding non-dimensional system.

This work analyzes a variant of a model introduced by K.R. Rajagopal describing a flow through a deformable porous solid where the viscosity of the fluid and drag coefficient depend on the fluid’s pressure. The variant consists in truncating and regularizing the pressure in space by convolution and in time by convolution plus retardation. For this variant, a priori estimates and existence of solutions are established.

The main purposes of the present paper are to present the mathematical and algorithmic aspects of the ANM/FEM numerical model and to show how it is applied to analyze elastic and thermo-elastic nonlinear solid mechanical problems. ANM is a robust continuation method based on a perturbation technique for solving nonlinear problems dependent on a loading parameter. Historically, this technique has been successfully applied to problems in various fields of solid and fluid mechanics. This paper shows how ANM is used to solve nonlinear elastic and nonlinear thermo-elastic problems involving elastic behavior and geometrical nonlinearities. The implementation of ANM for FEM in the FreeFEM++ language is then presented. The FEM software development platform, called FreeFEM++, is structured to work with variational formulations and, therefore, is well adapted to implement ANM for instability problems in solid mechanics. In order to illustrate the great efficiency of FreeFEM++, scripts will be presented for computing the different steps of ANM continuation for solid elastic structures, considering simple geometries subjected to conservative loading. For the purpose of validation, the problem of a cantilever subjected to an applied force is presented. Next, the new numerical model is applied to study wrinkles appearing in a planar film/substrate system that is subjected to compressive surface forces at the lateral faces of the film. Finally, the model is applied to a spherical film/substrate system subjected to thermo-elastic shrinkage. In both cases, the ANM/FEM prediction method, together with a Newton–Riks correction (if needed), identifies the equilibrium paths efficiently, especially after the post-buckling regime.

We present a finite element toolbox for the computation of Bogoliubov-de Gennes modes used to assess the linear stability of stationary solutions of the Gross-Pitaevskii (GP) equation. Applications concern one (single GP equation) or two-component (a system of coupled GP equations) Bose-Einstein condensates in one, two and three dimensions of space. An implementation using the free software FreeFem++ is distributed with this paper. For the computation of the GP stationary (complex or real) solutions we use a Newton algorithm coupled with a continuation method exploring the parameter space (the chemical potential or the interaction constant). Bogoliubov-de Gennes equations are then solved using dedicated libraries for the associated eigenvalue problem. Mesh adaptivity is proved to considerably reduce the computational time for cases implying complex vortex states. Programs are validated through comparisons with known theoretical results for simple cases and numerical results reported in the literature.

The Dual Characteristic-Galerkin method (DCGM) is conservative, precise and experimentally positive. We present the method and prove convergence and $L^2$-stability in the case of Neumann boundary conditions. In a 2D numerical finite element setting (FEM), the method is compared to Primal Characteristic-Galerkin (PCGM), Streamline upwinding (SUPG), the Dual Discontinuous Galerkin method (DDG) and centered FEM without upwinding. DCGM is difficult to implement numerically but, in the numerical context of this note, it is far superior to all others.

We present finite-element numerical algorithms for the identification of vortices in quantum fluids described by a macroscopic complex wave function. Their implementation using the free software FreeFem++ is distributed with this paper as a post-processing toolbox that can be used to analyse numerical or experimental data. Applications for Bose-Einstein condensates (BEC) and superfluid helium flows are presented. Programs are tested and validated using either numerical data obtained by solving the Gross-Pitaevskii equation or experimental images of rotating BEC. Vortex positions are computed as topological defects (zeros) of the wave function when numerical data are used. For experimental images, we compute vortex positions as local minima of the atomic density, extracted after a simple image processing. Once vortex centers are identified, we use a fit with a Gaussian to precisely estimate vortex radius. For vortex lattices, the lattice parameter (inter-vortex distance) is also computed. The post-processing toolbox offers a complete description of vortex configurations in superfluids. Tests for two-dimensional (giant vortex in rotating BEC, Abrikosov vortex lattice in experimental BEC) and three-dimensional (vortex rings, Kelvin waves and quantum turbulence fields in superfluid helium) configurations show the robustness of the software. The communication with programs providing the numerical or experimental wave function field is simple and intuitive. The post-processing toolbox can be also applied for the identification of vortices in superconductors.

To study the temperature in a gas subjected to electromagnetic radiations, one may use the Radiative Transfer equations coupled with the Navier-Stokes equations. The problem has 7 dimensions; however with minimal simplifications it is equivalent to a small number of integro-differential equations in 3 dimensions. We present the method and a numerical implementation using an H-matrix compression scheme. The result is a very fast: 50K physical points, all directions of radiation and 680 frequencies require less than 5 minutes on an Apple M1 Laptop. The method is capable of handling variable absorptioN and scattering functionS of spatial positions and frequencies. The implementation is done using htool, a matrix compression library interfaced with the PDE solver freefem++. Applications to the temperature in the French Chamonix valley is presented at different hours of the day with and without snow / clouds and with a variable absorption taken from the Gemini measurements. The result is precise enough to assert temperature differences due to increased absorption in the vibrational frequency subrange of greenhouse gasses.

This paper presents a method to solve the mechanical problems undergoing finite deformations and the contact problems without friction, between an hyperelastic body and an obstacle. The main idea is to formulate the contact problem into a constrained minimization one. The constraints are written in a simple form which makes the interior point method very useful to solve the problem. Finally, the FreeFEM and interior Point OPTimizer (IPOPT) software are used to compute and solve the contact problem. Our method is validated against several benchmarks and used on an industrial application example.

Multi-type birth-death (MTBD) models are phylodynamic analogies of compartmental models in classical epidemiology. They serve to infer such epidemiological parameters as the average number of secondary infections R-e and the infectious time from a phylogenetic tree (a genealogy of pathogen sequences). The representatives of this model family focus on various aspects of pathogen epidemics. For instance, the birth-death exposed-infectious (BDEI) model describes the transmission of pathogens featuring an incubation period (when there is a delay between the moment of infection and becoming infectious, as for Ebola and SARS-CoV-2), and permits its estimation along with other parameters. With constantly growing sequencing data, MTBD models should be extremely useful for unravelling information on pathogen epidemics. However, existing implementations of these models in a phylodynamic framework have not yet caught up with the sequencing speed. Computing time and numerical instability issues limit their applicability to medium data sets (<= 500 samples), while the accuracy of estimations should increase with more data. We propose a new highly parallelizable formulation of ordinary differential equations for MTBD models. We also extend them to forests to represent situations when a (sub-)epidemic started from several cases (e.g., multiple introductions to a country). We implemented it for the BDEI model in a maximum likelihood framework using a combination of numerical analysis methods for efficient equation resolution. Our implementation estimates epidemiological parameter values and their confidence intervals in two minutes on a phylogenetic tree of 10,000 samples. Comparison to the existing implementations on simulated data shows that it is not only much faster but also more accurate. An application of our tool to the 2014 Ebola epidemic in Sierra-Leone is also convincing, with very fast calculation and precise estimates. As MTBD models are closely related to Cladogenetic State Speciation and Extinction (ClaSSE)-like models, our findings could also be easily transferred to the macroevolution domain.

In this work, we consider a rational approximation of the exponential function to design an algorithm for computing matrix exponential in the Hermitian case. Using partial fraction decomposition, we obtain a parallelizable method, where the computation reduces to independent resolutions of linear systems. We analyze the effects of rounding errors on the accuracy of our algorithm. We complete this work with numerical tests showing the efficiency of our method and a comparison of its performances with Krylov algorithms.

The aim of this paper is to present an algorithm to solve frictional contact problems by considering the Coulomb’s criterion. As it is known, the frictional contact problem using Coulomb’s criterion has no minimization principle behind. However in order to use algorithms based on minimization methods, the frictional contact problem is written as an optimization one, more specifically as a sequence of Tresca contact problems. Moreover a family of regularization functions is introduced in order to regularize the non-smooth character of the Tresca criterion, which in some cases can have an experimental justifications. As each minimization problem becomes smooth enough, the interior point method is used to solve the generated optimization problem, which has some advantages when the non-penetration constraints are imposed in a symmetrical manner.

This paper presents a generic framework for the numerical simulation of transformation-diffusion processes in complex volume geometric shapes. This work follows a previous one devoted to the simulation of microbial degradation of organic matter in porous system at microscopic scale. We generalized and improved the MOSAIC method significantly and thus yielding a much more generic and efficient numerical simulation scheme. In particular, regarding the simulation of diffusion processes from the graph, in this study we proposed a completely explicit and semi-implicit numerical scheme that can significantly reduce the computational complexity. We validated our method by comparing the results to the one provided by classical Lattice Boltzmann Method (LBM) within the context of microbial decomposition simulation. For the same datasets, we obtained similar results in a significantly shorter computing time (i.e., 10-15 minutes) than the prior work (several hours). Besides the classical LBM method takes around 3 weeks computing time.

Scalability of parallel solvers for problems with high heterogeneities relies on adaptive coarse spaces built from generalized eigenvalue problems in the subdomains. The corresponding theory is powerful and flexible but the development of an efficient parallel implementation is challenging. We report here on recent advances in adaptive coarse spaces and on their open source implementations.

This paper presents an algorithm to solve mechanical contact problems between two bodies or more, for linear elastic and finite deformation problems. The contact problem is considered as a minimization problem of an energy. The interior point method is used to solve the minimization problem. This algorithm is symmetric and the user no longer needs to specify a slave body and a master one. The algorithm was developed using FreeFEM and IPOPT software.

In this article, we study the thermal instability that appears from time to time while printing using a 3D printer. To solve the semi-discretized problem at each time-step, we use a scalable parallel algorithm based on a two-level Optimized Restricted Additive Schwarz (ORAS) domain decomposition preconditioner for GMRES. Parallel scalability tests are conducted with comparison against the parallel direct solver MUMPS and the one-level Schwarz method, which show lack of robustness for larger number of processors. 2D numerical tests illustrate that the number of iterations to reach GMRES convergence depends on the state of the physical simulation during time, and that the second level of preconditioning is needed to achieve robustness.

Abstract We derive optimal reliability and efficiency of a posteriori error estimates for the steady Stokes problem, with a nonhomogeneous Dirichlet boundary condition, solved by a stable enriched Galerkin scheme (EG) of order one on triangular or quadrilateral meshes in ℝ2, and tetrahedral or hexahedral meshes in ℝ3.

The microscale physical characteristics of microbial habitats considerably affect the decomposition of organic matter in soils. One of the challenges is to identify microheterogeneities in soil that can explain the extent of carbon mineralization. The aim of this study was therefore to identify descriptors of mu m-scale soil heterogeneity that can explain CO2 fluxes obtained at the mm scale. A suite of methods and models that visualize soil heterogeneity at scales relevant to microorganisms has been developed over the last decade. Among the existing 3D models that simulate microbial activity in soils, Mosaic is able to simulate, within a short computation time, the microbial degradation of organic matter at the microhabitat scale in soil using real 3D images of soil porosity. Our approach was to generate scenarios of carbon mineralization for various microscale environmental conditions and determine how the descriptors of soil structure could explain CO2 evolution. First, we verified that the simulated diffusion of solutes in the soil samples obtained with Mosaic were the same as those obtained using the same parameter set from a robust 3D model based on a lattice Boltzmann approach. Then, we ran scenarios considering different soil pore architectures, water saturations and microorganism and organic matter placements. We found that the CO2 emissions simulated for the different scenarios could be explained by the distance between microorganisms and organic matter, the diffusion of the substrate and the concentration of the available substrate. For some of the scenarios, we proposed a descriptor of accessibility based on the geodesic distance between microorganisms and organic matter weighted by the amount of organic matter. This microscale descriptor is correlated to the simulated CO2 flux with a correlation coefficient of 0.69. Highlights Does the microscopic soil organisation explain the macroscopic mineralisation fluxes ? We present a new descriptor based on the geodesic distances between organic matter and microorganisms. We found a correlation between the descriptor of mu m-heterogeneity and the mineralization fluxes. Other scenarios should be carried out under wider environmental mu m-conditions to confirm our results.