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.
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.
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.
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.
pcmsolver chem An API for the Polarizable Continuum Model.
phono3py chem 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.
wannier90 chem Wannier90 is a package to calculate maximally-localised Wannier functions.

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