Software Packages
R is a free software environment for statistical computing and graphics.
Modules
module avail R
- or -
module load R/3.2.0
Usage and Documentation
https://www.r-project.org
CP2K is a 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. The version installed, is linked against the Intel compiler for increased performance.
Modules
N/A
Usage and Documentation
GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) method and the atomic simulation environment (ASE)
Modules
gpaw/intel-0.11
Usage and Documentation
LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. IT includes potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems and can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale.
Modules
lammps/mvapich2
- or -
lammps/openmpi
Usage and Documentation
SageMath is a free open-source mathematics software system licensed under the GPL. It builds on top of many existing open-source packages: NumPy, SciPy, matplotlib, Sympy, Maxima, GAP, FLINT, R and many more.
Modules
N/A
Usage and Documentation
ORCA (Quantum Chemistry Program) is an ab initio quantum chemistry program package that contains modern electronic structure methods including density functional theory, many-body perturbation, coupled cluster theories, multireference, and semiempirical methods. Its main field of application is larger molecules, transition metal complexes, and their spectroscopic properties. Access to ORCA is restricted.
Modules
- or -
module load orca/3.0.3
Usage and Documentation
DL_POLY is a general purpose classical molecular dynamics (MD) simulation software developed at Daresbury Laboratory by I.T. Todorov and W. Smith. Access to DL-POLY is restricted.
Modules
- or -
module load dlpoly/intel-4.0.7
Usage and Documentation
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.
There are multiple (parallel) versions of SIESTA installed:
- SIESTA version 4.0b-485
- SIESTA version 3.2-pl-5 and
- SIESTA version 3.08 with DFT+U functionality
Modules
- or -
module load siesta/intel/3.2-pl-5 -or - module load siesta/intel/4.0b-485 -or - siesta/intel/308-ldau
Usage and Documentation
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.
Modules
- or -
module load qe/intel/5.2.1
- or -
module load qe/intel/5.3.0
- or -
module load qe/intel/6.2.1
Usage and Documentation
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
Modules
- or -
module load gromacs/intel-5.1.2
- or -
module load gromacs/gnu-5.1.2
Usage and Documentation
QMCPACK, is a modern high-performance open-source Quantum Monte Carlo (QMC) simulation code. Its main applications are electronic structure calculations of molecular, quasi-2D and solid-state systems. Variational Monte Carlo (VMC), diffusion Monte Carlo (DMC) and a number of other advanced QMC algorithms are implemented. By directly solving the Schrodinger equation, QMC methods offer greater accuracy than methods such as density functional theory, but at a trade-off of much greater computational expense.
Modules
- or -
module load qmcpack/4-4-16.r6854-gnu
- or -
module load qmcpack/4-4-16.r6854-intel
Note: There are multiple builds installed, qmcpack_std (standard qmcPACK standard version, MPI and OpenMP enabled) and qmcpack_cuda (CUDA version)
Usage and Documentation
BigDFT is a DFT massively parallel electronic structure code (GPL license) using a wavelet basis set. Wavelets form a real space basis set distributed on an adaptive mesh (two levels of resolution in our implementation). GTH or HGH pseudopotentials are used to remove the core electrons.
Modules
- or -
module load bigdft/1.7.7-gnu-cuda
- or -
module load bigdft/1.7.7-intel-cuda
Usage and Documentation
