Chemistry

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.

List of Chemistry Packages

To get an up-to-date list of the installed chemistry applications, log on to Rivanna and run the

module keyword chem

command in a terminal window.  Most of these packages do not have pages at the ARCS Website but we have provided links for those that do; this is not part of the module command's output.  The resulting package list will be similar to this:

---------------------------------------------------------------------
The following modules match your search criteria: "chem"
---------------------------------------------------------------------
 
 abinit: abinit/8.2.2

    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.

  chemps2: chemps2/1.8
    CheMPS2 is a scientific library which contains a spin-adapted
    implementation of the density matrix renormalization group (DMRG) for
    ab initio quantum chemistry.

  cp2k: cp2k/5.1
    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: gaussian/g16, gaussian/grads16
    Gaussian is a suite of electronic-structure codes.

  gromacs: gromacs/5.1.2
    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: hoomd/2.3.5
    HOOMD-blue is a general-purpose particle simulation toolkit. It scales
    from a single CPU core to thousands of GPUs.

  lammps: lammps/20180822
    LAMMPS is a classical molecular dynamics code, and an acronym for
    Large-scale Atomic/Molecular Massively Parallel Simulator.

  libint: libint/1.1.5, libint/2.4.2
    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: pcmsolver/1.1.4
    An API for the Polarizable Continuum Model.

  plumed: plumed/2.4.0
    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: quantumespresso/5.4.0, quantumespresso/6.1, ...
    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).

  shengbte: shengbte/1.1.1
    ShengBTE is a software package for solving the Boltzmann Transport
    Equation for phonons.

  siesta: siesta/4.1-b2
    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: thirdorder/1.1.1-py3
    Python package for creating input for ShengBTE.

  wannier90: wannier90/2.1.0
    Wannier90 is a package to calculate maximally-localised Wannier
    functions.

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

module spider lammps/20180822

Output:

----------------------------------------------------------------------------
  lammps: lammps/20180822
----------------------------------------------------------------------------
    Description:
      LAMMPS is a classical molecular dynamics code, and an acronym for
      Large-scale Atomic/Molecular Massively Parallel Simulator.

    This module can be loaded directly: module load lammps/20180822

    Additional variants of this module can also be loaded after loading the foll
owing modules:

      icc/.16.0  intelmpi/16.0
      ifort/.16.0  intelmpi/16.0
      intel/16.0  intelmpi/16.0
 
    Help:
      
      Description
      ===========
      LAMMPS is a classical molecular dynamics code, and an acronym for Large-sc
ale Atomic/Molecular Massively Parallel Simulator.
      
      Application class: chem
      
      
      More information
      ================
       - Homepage: http://lammps.sandia.gov/index.html