Category: Software

ELSI – ELectronic Structure Infrastructure provides and enhances scalable, open-source software library solutions for electronic structure calculations in materials science, condensed matter physics, chemistry, molecular biochemistry, and many other fields. ELSI focuses on methods that solve or circumvent eigenvalue problems in electronic structure theory. The ELSI infrastructure should also be useful for other challenging eigenvalue problems.

ELSI deals with the Kohn–Sham eigenvalue problem, which is central to Kohn–Sham density-functional theory, one of the most widely used methods in electronic structure. This problem is often the bottleneck in large scale calculations by high-performance computation and many different algorithms and strategies exist to tackle it. ELSI acts as a unified software interface to access different algorithms and their corresponding implementations. This greatly simplifies the implementation and optimal use of the different strategies.

This package contains software that will allow you to use existing neural network potential parameterizations to predict energies and forces (with standalone tools but also in conjunction with the MD software LAMMPS). In addition it is possible to train new neural network potentials with the provided training tools.

The CLIO code solves the Conditional Moment Closure transport equations for reacting scalars. These equations are PDE’s in three space directions, one or two sample space directions (mixture fraction, progress variable, two mixture fractions etc), and time. A fractional step approach is taken for the transport in real space, transport in conserved scalar space, and chemistry. Various stiff solvers have been used such as LIBSC, DVODE, VODEPK, LSODE, CHEMEQ, and various chemical schemes can be implemented. CLIO has been interfaced with various CFD codes in RANS and LES such as openFOAM, PRECISE_uns, FLUENT, and STAR-CD

CIAO performs DNS and LES with multiphysics effects (multiphase, combustion, soot, spark, …). It is a structured, arbitrary order, finite difference code with compressible and incompressible/low-Mach solvers. Moving meshes are supported and overset meshes can be used for local mesh refinement. Spatial and temporal staggering is used to increase the accuracy of stencils. The sub-filter model for the momentum equations is an eddy viscosity concept in form of the dynamic Smagorinsky model with Lagrangian averaging along fluid particle trajectories.The compressible solver uses a low-storage five-stage, explicit Runge-Kutta method for time integration. The low-Mach solver uses Crank-Nicolson time advancement along with an iterative predictor corrector scheme. The Poisson equation for the pressure is solved by the multi-grid HYPRE solver. Momentum equations are spatially discretized with central schemes of arbitrary order, while for scalar equations various different schemes (WENO, HOUC, QUICK, BQUICK, …) are available. Temperature and species equations are advanced by utilizing a Strang operator splitting. The chemistry operator uses a time-implicit backward difference method (CVODE).

PRECISE-UNS is a finite volume based unstructured CFD solver for turbulent multi-phase and reacting flows. It is a pressure-based code, which uses the pressure correction scheme / PISO scheme to achieve pressure velocity coupling. It is applicable to both low-Mach number and fully compressible flows. Discretisation in time and space is up to second order. The linearized equations are solved using various well-known libraries such as PETSc, HYPRE and AGMG. Several turbulence models are available: k-epsilon, k-ω-SST, RSM, SAS, LES. Different combustion models are available, ranging from the classical conserved scalar (flamelet) models and global reaction mechanism, to FGM and detailed chemistry. To model the interaction of chemistry and turbulence, EBU, Presumed PDF, ATF and Eulerian stochastic field PDF closures are available. To model emissions NOx and two equations and hmom soot models are available. In order to model liquid fuel, a Lagrangian spray model is available.

DISCO solves the fully compressible Navier-Stokes equations for reacting flows with detailed chemical kinetics on rectangular domains. It employs a third-order low-storage Runge-Kutta scheme for time integration and compact higher-order finite-difference schemes for the spatial derivatives. The code is parallelized using domain decomposition and MPI. The code has been used to simulate turbulent expanding flame kernels and mixing layers. Besides detailed reaction mechanisms, it can also use FGM tabulated chemistry.

JAGUAR is a new code, still under development, that aims to reach high accuracy on unstructured grids with high computing efficiency. The numerical approach that appears most promising for these objectives is Spectral Differences with possibility of h/p refinement. The code solves fully compressible, multi-species flow equations, reacting or non-reacting.

The AVIP code is devoted to the resolution of cold plasmas, as encountered in ignitors such as NRP (Nano-Repetitive Pulse Discharge). It is based on a fluid formulation taking into account the out-of-equilibrium nature of plasmas, and is coupled to a Poisson equation to solve the electric field (using libraries PETSC or MAPHYS) associated to sparking systems. The simulation of plasma requires the resolution of transport equations for electrons, ions and neutrals, including complex chemistry. AVIP is able today to compute 2D streamers and gives results in good agreement with the literature

YALES2 aims at the solving of two-phase combustion from primary atomization to pollutant prediction on massive complex meshes. It is able to handle efficiently unstructured meshes with several billions of elements, thus enabling the Direct Numerical Simulation and Large-Eddy Simulation of laboratory and semi-industrial configurations. The recent developments are focused on the dynamic mesh adaptation of tetrahedral-based massive meshes for fronts and interfaces.

The Common Workflow Language (CWL) is a specification for describing analysis workflows and tools in a way that makes them portable and scalable across a variety of software and hardware environments, from workstations to cluster, cloud, and high performance computing (HPC) environments. CWL is designed to meet the needs of data-intensive science, such as Bioinformatics, Medical Imaging, Astronomy, Physics, and Chemistry. CWL is developed by a multi-vendor working group consisting of organizations and individuals aiming to enable scientists to share data analysis workflows. The CWL project is maintained on Github and we follow the Open-Stand.org principles for collaborative open standards development. Legally, CWL is a member project of Software Freedom Conservancy and is formally managed by the elected CWL leadership team, however every-day project decisions are made by the CWL community which is open for participation by anyone. CWL builds on technologies such as JSON-LD for data modeling and Docker for portable runtime environments.

The Common Workflow Language (CWL) is a community-developed specification for interoperable scientific workflows, supported by multiple workflow engine vendors and open source projects. Started as a third-year project at The University of Manager and further developed as part of the BioExcel project, the CWL Viewer is available to visualize any CWL workflow definitions, show their annotations and composition.

The public CWL Viewer instance has become the de facto standard web visualization tool for workflows within the larger CWL community – the list of known workflows shows more than 2000 individual workflows have been visualized.

In 2017 the CWL Viewer was presented at the ISMB/ECCB conference where it won the F1000 Best Poster Award. The development and hosting of CWL Viewer is now being transitioned to Curii Corporation, an industry partner in the CWL project that is developing the Arvados platform.