Scientific Software Packages

This page provides links to the pages describing a number of the individual software packages installed centrally on ARCHER. The pages contain information on running jobs (including example job submission scripts).

Build and Run Instructions GitHub Repository

New compile and run instructions are now being added to a public GitHub repository at:

and we are migrating all current compile instructions to this repository. Links in the individual pages below will be updated to point to the new instructions and notes as they are added.

Contributing to the GitHub repository

We are happy to accept contributions to the repository of build and run instructions ia pull requests.

To contribute to this repository, first you have to fork it on GitHub and clone it to your machine, see Fork a Repo for the GitHub documentation on this process.

Once you have made your changes and updated your Fork on GitHub you will need to Open a Pull Request.

Amber/PMEMD A package of molecular simulation programs and analysis tools.
abinit ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis. ABINIT also includes options to optimize the geometry according to the DFT forces and stresses, or to perform molecular dynamics simulations using these forces, or to generate dynamical matrices, Born effective charges, and dielectric tensors, based on Density-Functional Perturbation Theory, and many more properties.
CASTEP A software package which uses density functional theory to provide a good atomic-level description of all manner of materials and molecules.
CESM Community Earth System Model, or CESM, is a fully-coupled, community, global climate model that provides state-of-the-art computer simulations of the Earth's past, present, and future climate states.
ChemShell A Tcl-based Chemistry code focusing on hybrid QM/MM calculations with support for standard quantum chemical or force field calculations.
Code_Saturne Code_Saturne solves the Navier-Stokes equations for 2D, 2D-axisymmetric and 3D flows, steady or unsteady, laminar or turbulent, incompressible or weakly dilatable, isothermal or not, with scalars transport if required. Several turbulence models are available, from Reynolds-Averaged models to Large-Eddy Simulation models. In addition, a number of specific physical models are also available as "modules": gas, coal and heavy-fuel oil combustion, semi-transparent radiative transfer, particle-tracking with Lagrangian modeling, Joule effect, electrics arcs, weakly compressible flows, atmospheric flows, rotor/stator interaction for hydraulic machines.
COSA COSA is a Computational Fluid Dynamics (CFD) suite of solvers of the Euler, laminar and turbulent compressible Navier-Stokes (NS) equations. All solvers are based on a finite volume discretisation of the physical domain by means of structured multi-block grids.
CP2K A freely available program to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials.
CPMD A parallelized plane wave/pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics.
CRYSTAL CRYSTAL is a general-purpose program for the study of crystalline solids. The CRYSTAL program computes the electronic structure of periodic systems within Hartree Fock, density functional or various hybrid approximations (global, range-separated and double-hybrids). The Bloch functions of the periodic systems are expanded as linear combinations of atom centred Gaussian functions. Powerful screening techniques are used to exploit real space locality. Restricted (Closed Shell) and Unrestricted (Spin-polarized) calculations can be performed with all-electron and valence-only basis sets with effective core pseudo-potentials.
Desmond A software package developed to perform high-speed molecular dynamics simulations of biological systems.
DL_MESO A mesoscale simulation package providing dissipative particle dynamics and an implementation of the lattice Boltzmann equation (LBE) for complex fluids.
DL_POLY A general purpose molecular dynamics simulation package.
ELk An all-electron full-potential linearised augmented-plane wave (FP-LAPW) code with many advanced features. Written originally at Karl-Franzens-Universitt Graz as a milestone of the EXCITING EU Research and Training Network.
Exciting An all-electron full-potential computer package providing the variety of different related basis sets, subsumed as (linearized) augmented planewave + local orbital (L)APW+lo methods.
Fire Dynamics Simulator A computational fluid dynamics model of fire-driven fluid flow.
FEniCS A software collection for the automated solution of differential equations.
GAMESS GAMESS is a program for ab initio molecular quantum chemistry. Briefly, GAMESS can compute SCF wavefunctions ranging from RHF, ROHF, UHF, GVB, and MCSCF. Correlation corrections to these SCF wavefunctions include Configuration Interaction, second order perturbation Theory, and Coupled-Cluster approaches, as well as the Density Functional Theory approximation.
GAMESS-UK GAMESS-UK is the general purpose ab initio molecular electronic structure program for performing SCF-, DFT- and MCSCF-gradient calculations, together with a variety of techniques for post Hartree Fock calculations
GPAW GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) method and the atomic simulation environment (ASE).
GROMACS GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.
GS2 A package to study gyro-kinetic turbulence in fusion experiments and astrophysical plasmas.
LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) a classical molecular dynamics code.
Molpro Molpro is a complete system of ab initio programs for molecular electronic structure calculations, designed and maintained by H.-J. Werner and P. J. Knowles, and containing contributions from a number of other authors. As distinct from other commonly used quantum chemistry packages, the emphasis is on highly accurate computations, with extensive treatment of the electron correlation problem through the multiconfiguration-reference CI, coupled cluster and associated methods.
NAG Library The NAG Library provides a collection of numerical and statistical algorithms which can be embedded into your codes on ARCHER at compile time.
NAMD A parallel molecular dynamics application designed to simulate large bio-molecular systems. It is developed and maintained by the University of Illinois at Urbana-Champaign.
NCIPLOT NCIPLOT is a program that enables the computation and graphical visualisation of inter- and intra-molecular non-covalent interactions (hydrogen bonds, ?-? interactions, ...) in systems ranging from small dimers to large biomolecules.
NWChem 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. The NWChem software can handle: Biomolecules, nanostructures, and solid-state; From quantum to classical, and all combinations; Gaussian basis functions or plane-waves; Scaling from one to thousands of processors; Properties and relativity.
ONETEP ONETEP (Order-N Electronic Total Energy Package) is a linear-scaling code for quantum-mechanical calculations based on density-functional theory
OpenFOAM OpenFOAM is an open-source toolbox for computational fluid dynamics. OpenFOAM consists of generic tools to simulate complex physics for a variety of fields of interest, from fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics, electromagnetism and the pricing of financial options. The core technology of OpenFOAM is a flexible set of modules written in C++. These are used to build solvers and utilities to perform pre- and post-processing tasks ranging from simple data manipulation to visualisation and mesh processing.
Paraview Paraview is a data visualisation and analysis package. Whilst ARCHER compute or login nodes do not have graphics cards installed in them paraview is installed so the visualisation libraries and applications can be used to post-process simulation data. To this end the pvserver application has been installed, along with the paraview libraries and client application.
PLUMED PLUMED is a plugin that works with a large number of molecular dynamics codes. It can be used to analyse features of the dynamics on-the-fly or to perform a wide variety of free energy methods.
Quantum Espresso Quantum Espresso is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.
SIESTA (Spanish Initiative for Electronic Simulations with Thousands of Atoms) is a program to perform electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids.
SLEPc (Scalable Library for Eigenvalue Problem Computations) a library for parallel computation of eigenvalues and eigenvectors. Based on PETSc. Note: not centrally installed as a module, only build instructions provided.
TINKER The TINKER molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers.
VASP A package for ab initio, quantum-mechanical, molecular dynamics simulations.
WIEN2k WIEN2k allows to perform electronic structure calculations of solids using density functional theory. It is based on the full-potential (linearized) augmented plane-wave and local orbitals method, one among the most accurate schemes for band structure calculations.
WRF WRF is the Weather Research and Forecasting model.