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We present and distribute a parallel finite-element toolbox written in the free software FreeFem for computing the Bogoliubov-de Gennes (BdG) spectrum of stationary solutions to one- and two-component Gross-Pitaevskii (GP) equations, in two or three spatial dimensions. The parallelization of the toolbox relies exclusively upon the recent interfacing of FreeFem with the PETSc library. The latter contains itself a wide palette of state-of-the-art linear algebra libraries, graph partitioners, mesh generation and domain decomposition tools, as well as a suite of eigenvalue solvers that are embodied in the SLEPc library. Within the present toolbox, stationary states of the GP equations are computed by a Newton method. Branches of solutions are constructed using an adaptive step-size continuation algorithm. The combination of mesh adaptivity tools from FreeFem with the parallelization features from PETSc makes the toolbox efficient and reliable for the computation of stationary states. Their BdG spectrum is computed using the SLEPc eigenvalue solver. We perform extensive tests and validate our programs by comparing the toolbox's results with known theoretical and numerical findings that have been reported in the literature., Comment: arXiv admin note: text overlap with arXiv:2303.05350

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., Comment: 7 figures

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.

Numerical methods for solving the Navier-Stokes equations for classical (or normal) viscous fluids are well established. This is also the case for the Gross-Pitaevskii equation, governing quantum inviscid flows (or superfluids) in the zero temperature limit. In quantum flows, like liquid helium II at intermediate temperatures between zero and 2.17 K, a normal fluid and a superfluid coexist with independent velocity fields. The most advanced existing models for such systems use the Navier-Stokes equations for the normal fluid and a simplified description of the superfluid, based on the dynamics of quantized vortex filaments, with ad hoc reconnection rules. There was a single attempt (C. Coste, The European Physical Journal B - Condensed Matter and Complex Systems, 1998) to couple Navier-Stokes and Gross-Pitaevskii equations in a global model intended to describe the compressible two-fluid liquid helium II. We present in this contribution a new numerical model to couple a Navier-Stokes incompressible fluid with a Gross-Pitaevskii superfluid. Coupling terms in the global system of equations involve new definitions of the following concepts: the regularized superfluid vorticity and velocity fields, the friction force exerted by quantized vortices to the normal fluid, the covariant gradient operator in the Gross-Pitaevskii based on a slip velocity respecting the dynamics of vortex lines in the normal fluid. A numerical algorithm based on pseudo-spectral Fourier methods is presented for solving the coupled system of equations.Finally, we numerically test and validate the new numerical system against well-known benchmarks for the evolution in a normal fluid of different types or arrangements of quantized vortices (vortex crystal, vortex dipole and vortex rings). The new coupling model opens new possibilities to revisit and enrich existing numerical results for complex quantum fluids., Comment: 32 pages, 7 figures

Comprehension of metabolic pathways is considerably enhanced by metabolic flux analysis (MFA-ILE) in isotope labeling experiments. The balance equations are given by hundreds of algebraic (stationary MFA) or ordinary differential equations (nonstationary MFA), and reducing the number of operations is therefore a crucial part of reducing the computation cost. The main bottleneck for deterministic algorithms is the computation of derivatives, particularly for nonstationary MFA. In this article we explain how the overall identification process may be speeded up by using the adjoint approach to compute the gradient of the residual sum of squares. The proposed approach shows significant improvements in terms of complexity and computation time when it is compared with the usual (direct) approach. Numerical results are obtained for the central metabolic pathways of Escherichia coli and are validated against reference software in the stationary case. The methods and algorithms described in this paper are included in the sysmetab software package distributed under an Open Source license at http://forge.scilab.org/index.php/p/sysmetab/., Comment: Preprint submitted to IEEE/ACM Transactions on Computational Biology and Bioinformatics

In this paper, we perform a comparison of two approaches for the parallelization of an existing, free software, FullSWOF 2D (http://www. univ-orleans.fr/mapmo/soft/FullSWOF/ that solves shallow water equations for applications in hydrology) based on a domain decomposition strategy. The first approach is based on the classical MPI library while the second approach uses Parallel Algorithmic Skeletons and more precisely a library named SkelGIS (Skeletons for Geographical Information Systems). The first results presented in this article show that the two approaches are similar in terms of performance and scalability. The two implementation strategies are however very different and we discuss the advantages of each one., Comment: 27 pages

The importance of the study of the propagation of a Tsunami wave came from the complex phenomenon and its natural disasters which represents a major risk for populations. To model this phenomena, we will consider a simplified Boussinesq system of Benjamin, Bona and Mahony type derived by D. Mitsotakis over a flat bottom then over a variable bottom in space and in time and apply this system, first, using a mesh generated using a photo of the Mediterranean sea, second, using a mesh generated using an imported xyz bathymetry for the sea near Java island and then we will consider a realistic example of the Tsunami wave near Java island which happened in 2006.We choose here to use FreeFem++ software which simplifies the construction of the domain, in particular, one of the advantage of FreeFem++ is that we can build a mesh using a photo and we can easily export bathymetric data in order to consider more realistic simulations where a special adapt mesh technique applied for these two methods is detailed in the sequel.

We consider here different family of Boussinesq systems in two space dimensions. These systems approximate the three-dimensional Euler equations and consist of three coupled nonlinear dispersive wave equations that describe propagation of long surface waves of small amplitude in ideal fluids over a horizontal bottom. We present here a FreeFem++ code aimed at solving numerically these systems where a discretization using P1 finite element for these systems was taken in space and a second order Runge-Kutta scheme in time. We give the detail of our code where we use a mesh adaptation technique. An optimization of the used algorithm is done and a comparison of the solution for different Boussinesq family is done too. The results we obtained agree with those of the literature.

FreeFem++ is an open source platform to solve partial differential equations numerically, based on finite element methods. It was developed at the Laboratoire Jacques-Louis Lions, Universit\'e Pierre et Marie Curie, Paris by Fr\'ed\'eric Hecht in collaboration with Olivier Pironneau, Jacques Morice, Antoine Le Hyaric and Kohji Ohtsuka. The FreeFem++ platform has been developed to facilitate teaching and basic research through prototyping. FreeFem++ has an advanced automatic mesh generator, capable of a posteriori mesh adaptation; it has a general purpose elliptic solver interfaced with fast algorithms such as the multi-frontal method UMFPACK, SuperLU . Hyperbolic and parabolic problems are solved by iterative algorithms prescribed by the user with the high level language of FreeFem++. It has several triangular finite elements, including discontinuous elements. For the moment this platform is restricted to the numerical simulations of problems which admit a variational formulation. We will give in the sequel an introduction to FreeFem++ which include the basic of this software. You may find more information throw this link http://www.freefem.org/ff++.