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Lists of the applications currently installed and ready to use in our HPC machines, including available versions.

 

ADF

Purpose: Density Functional Theory
Latest version: 2017.113
License: Proprietary License here
Website: https://www.scm.com/ extlink-icon

Amsterdam Density Functional (ADF) is a proprietary software suite for density functional theory (DFT) calculation of molecular systems, especially inorganic systems.

Amber

Purpose: Molecular Dynamics
Latest version: 14
Licence: Proprietary licence
Website: http://ambermd.org/ extlink-icon

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

Purpose: Finite Element Analysis
Latest version: 13.4
Licence: GNU GPL
Website: https://code-aster.org/spip.php?rubrique2 extlink-icon

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

Purpose: Ab initio
Latest version: 6.1
License: GNU GPL
Website: https://www.cp2k.org/ extlink-icon

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

Purpose: Fire Simulator
Latest version: 6.6.0
Licence: Open Source
Website: https://pages.nist.gov/fds-smv/ extlink-icon

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

Purpose: Electronic Structure Calculations
Latest version: 2018
Licence: Mixed - Free of charge research licence
Website: http://www.msg.ameslab.gov/gamess/ extlink-icon

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

Purpose: electronic Structure Calculations
Latest version: Gaussian16 B.01
License: Closed-source
Website: http://gaussian.com/ extlink-icon

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

Purpose: Molecular Dynamics
Latest version: 2018.1
License: GNU LGPL
Website: http://www.gromacs.org/ extlink-icon

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

Purpose: Molecular Dynamics
Latest version: 16Mar2018
License: GNU GPL
Website: http://lammps.sandia.gov/ extlink-icon

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.

NAMD

Purpose: Molecular Dynamics
Latest version: 2.12
License: Mixed - Free for non-commercial users
Website: http://www.ks.uiuc.edu/Research/namd/ extlink-icon

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

Purpose: Electronic Structure Calculations
Latest version: 6.8
License: EDL
Website: http://www.nwchem-sw.org/index.php/Main_Page extlink-icon

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

Purpose: Computational Fluid Dynamics
Latest version: 5.0
Licence: GNU GPL
Website: http://www.openfoam.com/ extlink-icon

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

Purpose: electronic Structure Calculations
Latest version: 4.0.0
License: Mixed - Free for academics; forbidden for commercial.
Website: https://orcaforum.cec.mpg.de/ extlink-icon

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

Purpose: Electronic structure, materials modelling
Latest version: 6.2.1
License: GNU GPL
Website: https://www.quantum-espresso.org/ extlink-icon

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

Purpose: Statistics and plotting
Latest version: 3.5.5
License: Open Source - GNU GPL
Website: https://www.r-project.org/ extlink-icon

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

Purpose: Ab initio electronic structure, Molecular Dynamics
Latest version: 4.0.1
License: Mixed - Free for academics users.
Website: https://departments.icmab.es/leem/siesta/ extlink-icon

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+

Purpose:  Fluid Dynamics & Engineering
Latest version: 12.06.011
License: Proprietary License here
Website: https://www.plm.automation.siemens.com/global/en/products/simcenter/STAR-CCM.html extlink-icon

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.

VASP

Purpose: ab initio Molecular Dynamics
Latest version: 5.4.1
License: Proprietary
Website: https://www.vasp.at/ extlink-icon

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.

WESTPA

Purpose: Molecular Dynamics
Latest version: 1.0 beta
License: GNU GPL
Website:  https://westpa.github.io/westpa/sphinx_index.html extlink-icon

WESTPA is a package for constructing and running stochastic simulations using the “weighted ensemble” approach of Huber and Kim (1996).

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