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Chemistry

Add new Chemistry Software

  • GPAW a density functional theory Python code based on the projector-augmented wave method.
  • GROMACSA versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion 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.
  • RELIONREgularised 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)
  • VASPA complex package for performing ab-initio quantum-mechanical molecular dynamics (MD) simulations using pseu­do­po­ten­tials or the projector-augmented wave method and a plane wave basis set.

  • ASE – The Atomic Simulation Environment – a set of tools and Python modules for setting up, manipulating, running, visualizing, and analyzing atomistic simulations.
  • GPAW – A density functional theory Python code based on the projector-augmented wave method. It uses real-space uniform grids and multi-grid methods, atom-centered basis functions, or plane waves. 
  • CP2K – A package for atomistic simulations of solid state, liquid, molecular, and biological systems offering a wide range of computational methods; see "module avail cp2k" 
  • 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. 
  • Quantum ESPRESSO – An integrated suite of codes for electronic structure calculations and materials modeling at the nanoscale, based on DFT, plane waves, and pseudopotentials. 
  • BandUP – Band unfolding for plane wave based electronic structure calculations. 

Data manipulation, tools and libraries

Add new Data Manipulation Software

  • CDOThe Climate Data Operators
  • ECCODESECMWF application programming interface
  • HDF5 Libraries and BinariesHDF5 - hierarchical data format
  • libtiffA 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
  • NCOThe NetCdf Operators
  • netCDFNetwork Common Data Form
  • OctaveAdd short Excerpt. This will be included in the Software list
  • pigzA parallel implementation of gzip for modern multi-processor, multi-core machine
  • PROJCartographic Projections Library 
  • RR - statistical computing and graphics
  • SzipSzip, fast and lossless compression of scientific data
  • The Unidata UDUNITS2 PackageConversion and manipulation of units

  • Boost – Boost C++ libraries
  • CGAL – The Computational Geometry Algorithms Library

Development tools, compilers, translators, languages, performance analysis

Add new Development/Debugging Tool or Compiler

  • antlrAnother Tool for Language Recognition
  • Arm DDTParallel debugger, including MPI/OpenMP programs.
  • Charm++Parallel Programming Framework
  • Patchelfa simple utility for modifying existing ELF executables and libraries.
  • PythonAn Overview over the different Python Versions available on our System
  • Valgrind instrumentation frameworkan instrumentation framework for building dynamic analysis tools

  • CMake – CMake build environment
  • GCC – GNU Compiler Collection for C, C++, Fortran, Go, Objc, Objc++ and Lto
  • OpenMPI – High Performance Message Passing Library

Engineering

Add Engineering Software

  • ABAQUSA Finite Element Analysis Package for Engineering Application
  • ANSYS CFXComputational fluid dynamics solver focused on turbo-machinery (vertex-centered FVM)
  • ANSYS FluentGeneral computational fluid dynamics solver (cell-centered FVM)
  • ANSYS MechanicalA Package for Coupled Physics Simulations
  • Foam-extendThe Open Source CFD Toolbox
  • How to bring your own license
  • OpenFOAMAn object-oriented Computational Fluid Dynamics(CFD) toolkit
  • STAR-CCM+A Package for Computational Fluid Dynamics Simulations

  • ParaViewAn interactive data analysis and visualisation tool with 3D rendering capability



Miscellaneous

Add new Miscellaneous Software

  • nocachenocache - minimize caching effects in lustre filesystems
  • Singularityenables users to have full control of their environment

  • texlive – LaTeX distribution, typesetting system
  • git – A fast, scalable, distributed revision control system 

Numerics

Add new Numerics Software

  • BLASBLAS (Basic Linear Algebra Subprograms)
  • FFTW3A C-subroutine library for computing discrete Fourier transforms
  • GSLThe GNU Scientific Library (GSL)- a numerical library for C and C++ programmers
  • MUMPSMUltifrontal Massively Parallel sparse direct Solver.
  • NFFTDiscrete Fourier transform (DFT) in one or more dimensions
  • ScaLAPACKScalable LAPACK
  • ScotchSoftware 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.

Visualisation

Add new Visualisation Software

  • Ferret - Data Visualization and Analysisyour ferret in large and complex gridded data sets. 
  • GraDSAn interactive desktop tool for easy access, manipulation, and visualization of earth science data
  • NCL
  • NcViewNcview - a visual browser for netCDF formated files. 
  • ParaViewAn interactive data analysis and visualisation tool with 3D rendering capability
  • pyfesom2Python library and tools for handling of FESOM2 ocean model output