Needs to be migrated
https://support.hlrn.de/home/view/System4/AtosSoftware
- BLAS
- Charm++
- GROMACS
- LAPACK
- MUMPS
- Numerics
- ParaView
- Python
- RELION
- STAR-CCM+
- Scotch
- Singularity
- VASP
- Valgrind
- libtiff
- pigz
Needs to be created
- ASE
- BandUP
- Boost
- CGAL
- CMake
- CPMD
- GCC → Quickstart Guide?
- LAMMPS
- MOLPRO
- NWChem
- OpenMPI → Quickstart Guide?
- PLUMED
- Quantum ESPRESSO
- TURBOMOLE
- texlive
Engineering
- Abaqus - only with own license — a Finite Element Analysis Package for Engineering Application
- Ansys Suite — The full Ansys Academic Multiphysics Campus Solution is available, e.g. Mechanical, CFX, Fluent, LS-Dyna, Electronic, SCADE (but not Lumerical, GRANTA).
- MATLAB - only with own license — a proprietary multi-paradigm programming language and numeric computing environment developed by MathWorks
- OpenFOAM — an object-oriented open source CFD toolkit
- STAR-CCM+ — a Package for Computational Fluid Dynamics Simulations
- Bring your own license — of any software from you own license server
- HDF5 libraries / binaries
- ParaView — An interactive data analysis and visualisation tool with 3D rendering capability
Chemistry
- CP2K — A package for atomistic simulations of solid state, liquid, molecular, and biological systems offering a wide range of computational methods with the mixed Gaussian and plane waves approaches.
- exciting — a full-potential all-electron code, employing linearized augmented planewaves (LAPW) plus local orbitals (lo) as basis set.
- Gaussian — a computational chemistry application provided by Gaussian Inc https://gaussian.com/.
- GPAW — a density functional theory Python code based on the projector-augmented wave method.
- GROMACS — a versatile package to perform molecular dynamics for systems with hundreds to millions of particles.
- NAMD — a parallel, object-oriented molecular dynamics code designed for high-performance simulations of large biomolecular systems using force fields.
- Octopus — a software package for density-functional theory (DFT), and time-dependent density functional theory (TDDFT)
- Quantum ESPRESSO — an integrated suite of codes for electronic structure calculations and materials modeling at the nanoscale, based on DFT, plane waves, and pseudopotentials.
- RELION — REgularised LIkelihood OptimisatioN is a stand-alone computer program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy(cryo-EM)
- SIESTA — “both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids.” SIESTA project https://siesta-project.org/siesta/About/overview.html
- TURBOMOLE — TURBOMOLE is a computational chemistry program that implements various quantum chemistry methods (ab initio methods). It was initially developed at the University of Karlsruhe.
- VASP — a first-principles code for electronic structure calculations and molecular dynamics simulations in materials science and engineering.
- Wannier90 — A program that calculates maximally-localised Wannier functions.
- Abinit
- ASE – The Atomic Simulation Environment – a set of tools and Python modules for setting up, manipulating, running, visualizing, and analyzing atomistic simulations.
- LAMMPS – A parallel, classical potential molecular dynamics code for solid-state materials, soft matter and coarse-grained or mesoscopic systems.
- TURBOMOLE – A program package for ab initio electronic structure calculations. (see "module avail turbomole" on the SMP cluster)
- NWChem – A general computational chemistry code with capabilities from classical molecular dynamics to highly correlated electronic structure methods, designed to run on massively parallel machines.
- MOLPRO – A comprehensive system of ab initio programs for advanced molecular electronic structure calculations.
- PLUMED – A tool for trajectory analysis and plugin for molecular dynamics codes for free energy calculations in molecular systems
- CPMD – A plane wave / pseudopotential implementation of DFT, designed for massively parallel ab-initio molecular dynamics.
- BandUP – Band unfolding for plane wave based electronic structure calculations.
Numerics
- BLAS — BLAS (Basic Linear Algebra Subprograms)
- FFTW3 — A C-subroutine library for computing discrete Fourier transforms
- GSL — The GNU Scientific Library (GSL)- a numerical library for C and C++ programmers
- MUMPS — MUltifrontal Massively Parallel sparse direct Solver.
- NFFT — Discrete Fourier transform (DFT) in one or more dimensions
- ScaLAPACK — Scalable LAPACK
- Scotch — Software package and libraries for sequential and parallel graph partitioning, static mapping, sparse matrix block ordering, and sequential mesh and hypergraph partitioning.
- METIS – A set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices.
- ParMETIS – An MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices.
- PETSc – Portable, Extensible Toolkit for Scientific Computation: widely used parallel numerical software library for partial differential equations and sparse matrix computations.
Program development tools, compilers, translators, languages, performance analysis
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Visualisation tools
Add new Visualisation Software
- Ferret - Data Visualization and Analysis — your ferret in large and complex gridded data sets.
- GraDS — An interactive desktop tool for easy access, manipulation, and visualization of earth science data
- NCL
- NcView — Ncview - a visual browser for netCDF formated files.
- ParaView — An interactive data analysis and visualisation tool with 3D rendering capability
- pyfesom2 — Python library and tools for handling of FESOM2 ocean model output
Tools and libraries for data manipulation
Add new Data Manipulation Software
- AEC library — Adaptive Entropy Coding library
- CDO — The Climate Data Operators
- ECCODES — ECMWF application programming interface
- HDF5 libraries / binaries — HDF5 - hierarchical data format
- libtiff — A software package containing a library for reading and writing _Tag Image File Format_(TIFF), and a small collection of tools for simple manipulations of TIFF images
- libz — A Massively Spiffy Yet Delicately Unobtrusive Compression Library
- NCO — The NetCdf Operators
- netCDF — Network Common Data Form
- pigz — A parallel implementation of gzip for modern multi-processor, multi-core machine
- PROJ — Cartographic Projections Library
- R — R - statistical computing and graphics
- Szip — Szip, fast and lossless compression of scientific data
- UDUNITS2 — Unidata UDUNITS2 Package, Conversion and manipulation of units
- Boost – Boost C++ libraries
- CGAL – The Computational Geometry Algorithms Library
Miscellaneous software packages
Add new Miscellaneous Software
- libcurl — curl - a tool for transferring data from or to a server
- nocache — nocache - minimize caching effects in lustre filesystems
- texlive – LaTeX distribution, typesetting system
- git – A fast, scalable, distributed revision control system