Overview

Many popular software packages for computational chemistry are available on Rivanna.

General considerations

Most computational chemistry packages utilize MPI for parallel execution. Accordingly, the Slurm job scripts should contain the following two SBATCH directives:

#SBATCH -N <M>                  # request M nodes (replace with a number)
#SBATCH --ntasks-per-node=<L>   # request L MPI processes per node

You should launch your program with srun as the MPI executor, for example for Quantum Espresso

srun pw.x -in mymol.in

Please see the page of the particular package you wish to use for more details.

VASP Users The Vienna Ab-Initio Simulation Package, is licensed by individual groups and we do not have a common installation. We have basic instructions for building VASP on Rivanna at its page.

Available Chemistry Software

To get an up-to-date list of the installed chemistry applications, log on to Rivanna and run the following command in a terminal window:

module keyword chem

To get more information about a specific module version, run the module spider command, for example:

module spider quantumespresso

List of Chemistry Software Modules

Module Category Description
abinit chem 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.
alamode chem ALAMODE is designed for analyzing lattice anharmonicity and lattice thermal conductivity of solids. By using an external DFT package such as VASP and Quantum ESPRESSO, you can extract harmonic and anharmonic force constants straightforwardly with ALAMODE. Using the anharmonic force constants, you can also calculate lattice thermal conductivity from first principles.
amber chem Amber (originally Assisted Model Building with Energy Refinement) is software for performing molecular dynamics and structure prediction.
amptorch chem AMPtorch is a PyTorch implementation of the Atomistic Machine-learning Package (AMP) code that seeks to provide users with improved performance and flexibility as compared to the original code. The implementation does so by benefiting from state-of-the-art machine learning methods and techniques to be optimized in conjunction with high-throughput supercomputers. AMPtorch is built on top of PyTorch Geometric and Skorch.
ase chem The Atomic Simulation Environment (ASE) is a set of tools and Python modules for setting up, manipulating, running, visualizing and analyzing atomistic simulations.
atat chem The Alloy-Theoretic Automated Toolkit (ATAT) is a generic name that refers to a collection of alloy theory tools
chemps2 chem CheMPS2 is a scientific library which contains a spin-adapted implementation of the density matrix renormalization group (DMRG) for ab initio quantum chemistry.
cp2k chem CP2K is a freely available (GPL) program, written in Fortran 95, 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.
gaussian chem Gaussian is a suite of electronic-structure codes.
gpumd chem GPUMD stands for Graphics Processing Units Molecular Dynamics. It is a general-purpose molecular dynamics (MD) code fully implemented on graphics processing units (GPUs).
gromacs chem 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.
hunspell chem Hunspell is a spell checker and morphological analyzer library and program designed for languages with rich morphology and complex word compounding or character encoding. Hunspell interfaces: Ispell-like terminal interface using Curses library, Ispell pipe interface, C++ class and C functions.
kim-api chem Open Knowledgebase of Interatomic Models. KIM is an API and OpenKIM is a collection of interatomic models (potentials) for atomistic simulations. This is a library that can be used by simulation programs to get access to the models in the OpenKIM database. This EasyBuild only installs the API, the models can be installed with the package openkim-models, or the user can install them manually by running kim-api-collections-management install user MODELNAME or kim-api-collections-management install user OpenKIM to install them all.
lammps chem LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS is a classical molecular dynamics simulation code designed to run efficiently on parallel computers.
lammps_flare chem Custom LAMMPS-Flare module for Paolucci group
libint chem Libint - a library for the evaluation of molecular integrals of many-body operators over Gaussian functions
libxc chem Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.
namd chem NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
ocp-models chem ocp-models is the modeling codebase for the Open Catalyst Project. It provides implementations of state-of-the-art ML algorithms for catalysis that take arbitrary chemical structures as input to predict energy / forces / positions
openbabel chem Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.
openmm chem OpenMM is a toolkit for molecular simulation using high performance GPU code.
orca chem ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects.
p4vasp chem Variation graphs provide a succinct encoding of the sequences of many genomes.
pcmsolver chem An API for the Polarizable Continuum Model.
phonopy chem Phonopy is an open source package of phonon calculations based on the supercell approach. Phono3py calculates phonon-phonon interaction and related properties using the supercell approach.
plumed chem PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes.
quantumespresso chem 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.
shengbte chem ShengBTE is a software package for solving the Boltzmann Transport Equation for phonons.
siesta chem SIESTA is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids.
thirdorder chem A Python script to help create input files for computing anhamonic interatomic force constants, harnessing the symmetries of the system to minimize the number of required DFT calculations. A second mode of operation allows the user to build the third-order IFC matrix from the results of those runs.
vasp chem The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling.
vmd chem VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
wannier90 chem Wannier90 is a package to calculate maximally-localised Wannier functions.
yaff chem Yaff stands for 'Yet another force field'. It is a pythonic force-field code.

Using a Specific Software Module

To use a specific software package, run the module load command. The module load command in itself does not execute any of the programs but only prepares the environment, i.e. it sets up variables needed to run specific applications and find libraries provided by the module.

After loading a module, you are ready to run the application(s) provided by the module. For example:

module load intel quantumespresso