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/6.3

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.
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.
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.
hoomd	chem	HOOMD-blue is a general-purpose particle simulation toolkit. It scales from a single CPU core to thousands of GPUs.
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 is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator.
libint	chem	Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.
namd	chem	NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
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 computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft).
thirdorder	chem	Python package for creating input for ShengBTE.
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 quantumespresso/6.3