Lists of the applications currently installed and ready to use in our HPC machines, including available versions.
Amsterdam Density Functional (ADF) is a proprietary software suite for density functional theory (DFT) calculation of molecular systems, especially inorganic systems.
ADF implements Kohn-Sham-type DFT calculations to finite molecular systems, in gas phase or in solution. It applies LDA, GGA, and in some cases hybrid and meta-GGA functionals, including relativistic effects, to Slater-type orbitals.
Amber is a collection of programs for setting-up, running and analysing molecular dynamics simulations.
Amber refers both to a collection of about 50 programs for building, configuring and minimising molecular structures, setting up force fields, running simulations, analysing trajectories, and computing system properties, and to a force field for biomolecules implemented by the Amber programs.
Code_Aster is a computer-assisted engineering suite, with a focus on finite element methods.
The core of Code_Aster is a finite element solver for structural analysis, with additional programs for thermal flows, linear and non-linear static and dynamic analysis, fatigue, damage and fracture tools and multi-physics coupling. A companion open source pre- and post-processor, Salome, is also available.
CP2K is a program for ab initio electronic structure calculations and molecular dynamics.
CP2K is geared towards, but not restricted to, massive parallel computations using mixed plane-wave/Gaussian bases and pseudopotentials. It can implement a variety of methods, including semiempirical, HF, DFT (LDA, GGA, meta-GGA, hybrid), MP2 and TD-DFT, for molecular and periodic systems.
FDS is a program for fire simulations.
FDS is a computational fluid dynamics (CFD) program which implements large eddy simulations (LES) for the analysis of fire evolution and fire-driven fluid flows, including smoke and heat transfer. Its companion program Smokeview allows for the visualisation and analysis of fire dynamics.
GAMESS is a program for ab initio molecular electronic structure calculations.
Functionality includes HF, GVB, MCSCF, CI, MP2, CC and DFT methods, excited states, geometry optimisation, vibrational frequencies, solvation effects, relativistic corrections, pseudopotentials and nuclear wavefunctions.
Gaussian is a program implementing a variety of computational chemistry methods.
The range of computational methods includes molecular mechanics, semi-empirical methods, Hartree-Fock SCF, Møller-Plesset perturbation theory, DFT methods, QM/MM calculations, CI methods and CC calculations. Calculations employing these methods can be carried out in order to optimise molecular geometry, electronic structure and derived chemical properties.
Gromacs is a program for general molecular dynamics, notable for its fast computation of 1-4 interactions.
It can implement regular molecular dynamics simulations using a variety of integrators, Langevin dynamics, energy minimisation, test-particle insertion, etc. It implements a variety of methods to calculate electrostatics and Van der Waals interactions, thermostats and barostats, 2- and 3-dimensional periodic boundary conditions, etc.
LAMMPS is a classical molecular dynamics application.
It performs atomistic or coarse-grained simulations of molecular, macromolecular and mesoscale systems with a variety of force fields.
MOLCAS is an electronic structure calculations package.
It provides a particular emphasis on multi-configurational methods for highly degenerated ground states. MOLCAS can implement methods for single determinant ground states (SCF, MP2, CC, DFT), but focuses on treating accurately highly degenerate states (excited states, heavy metals, transition states, etc.) through methods such as multi-configurational self-consistent field (MCSCF), complete active space (CASSCF), and including correlation effects via second-order perturbation theory (CASPT2).
NAMD is a molecular dynamics package.
NAMD implements standard MD capabilities (variety of integrators, thermostats, barostats, force field compatibility, PME electrostatics, timestep integration, replica exchange, free energy calculations, etc.).
NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters.
OpenFOAM is a software environment for computational fluid dynamics (CFD) and related computations.
OpenFOAM provides a C++ library and tools for setting up, meshing, solving, computing properties, and post-processing continuum mechanics, especially computational fluid dynamics. OpenFOAM includes solvers for a number of applications and provides an environment in which users can build their own.
ORCA is a program that implements HF, DFT, semi-empirical, and high level ab initio (CI and CC) methods with gaussian basis sets for electronic structure calculations.
Quantum ESPRESSO is a suite for electronic structure calculations and simulation of nanostructured materials.
The core of Quantum ESPRESSO are density functional theory (DFT) electronic calculations using plane-wave basis sets and pseudopotential.
R is a language and environment for statistical computing and plotting.
R implements tools for data analysis, array operators (especially matrices), I/O features, graphical output features, and a high-level language (S) for integrating all of them, including user-defined variables, loops, etc.
SIESTA is a program for ab initio electronic structure and molecular dynamics of solids and molecules.
SIESTA applies DFT hamiltonians (LDA, GGA) to strictly localized numerical basis sets and non-local pseudopotentials to obtain electronic structures. From these it can compute solid properties (band structure, DOS, k-space sampling, dielectric polarisation, phonons), perform Born-Oppenheimer molecular dynamics (NVT and NPT), and, in recent versions, Van der Waals potentials and ballistic electron transport properties (TranSIESTA).
STAR-CCM+ is a multiphysics simulation package.
Built around a core for simultaneous resolution of computational fluid dynamics and heat transfer, STAR-CCM+ includes multiphase simulation, polyhedral meshing of solids and fluids, a fuel cells package, phase changes, chemical reactions, electromagnetics, etc.
Vienna Ab-Initio Simulation Package (VASP) is a program for plane-wave ab initio molecular dynamics.
VASP is a package to perform Born-Oppenheimer ab initio molecular dynamics (MD) simulations, employing a plane-wave DFT approach (LDA, GGA, meta-GGA, hybrids) to electronic structure. It implements either Vanderbilt pseudopotentials or the projector-augmented wave (PAW) method and Pulay-Broyden convergence to compute the ground electronic state at each step, as opposed to Car-Parrinello molecular dynamics.
VMD (Visual Molecular Dynamics) is a visualization program to visualize, model and analyze biomolecular systems. Can generate PSF (Protein Structure File) files, perform live simulations unsing NAMD and modelize and analize sistems through its plugins. Is also fully compatible with the most part of Molecular file formats(PDB,PSF, CHARM,AMBER...).
The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis (WESTPA) is a high-performance framework for carrying out extended-timescale simulations of rare events with rigorous kinetics using the weighted ensemble algorithm of Huber and Kim (1996).