# Applications

This page summarizes applications available on NREL HPC systems by discipline. Not all software is available on every system. For a table that shows what system each software package is installed on, please see the Applications by System page. Hyperlinked titles link to NREL-specific information; hyperlinked package names in the description or on NREL-specific pages link to the development website.

Packages with "(ECOM)" in the description are supported by the Peregrine user community. To access these, be sure to modify your modules search path to include /nopt/nrel/ecom/modules.

## Chemistry

### Atomic Simulation Environment

A package of Python modules for manipulating atoms, analyzing simulations, and visualization.

### Amber

The Amber package (Assisted Model Building with Energy Refinement) is both a set of molecular mechanical force fields for the simulation of biomolecules, and a package of molecular simulation programs which includes source code and demos.

### CHARMM

CHARMM is a parallelized molecular dynamics package developed by investigators across the globe, including some at NREL. The package offers many accelerated dynamics schemes and analysis tools.

### GAMESS

GAMESS is a general *ab initio* quantum chemistry package.

### Gaussian

Gaussian 09 is the latest in the Gaussian series of programs for calculating molecular electronic structure and reactivity.

### GROMACS

Gromacs is a molecular dynamics package primarily designed for biomolecular systems.

### LAMMPS

LAMMPS is an open source classical molecular dynamics program distributed by Sandia National Laboratories, designed for massively parallel systems.

### NAMD

NAMD is a parallel molecular dynamics program designed for high performance simulation of large biomolecular systems. It scales to hundreds of cores for typical simulations and to more than 200,000 cores for the largest simulations.

### NWChem

NWChem is a highly scalable computational chemistry and materials science program developed and maintained by EMSL at the Pacific Northwest National Laboratory.

### Q-Chem

Q-Chem is a comprehensive *ab initio* quantum chemistry package for accurate predictions of molecular structures, reactivities, and vibrational, electronic and NMR spectra. Particular strengths of this package include advanced methods for excited states and non-adiabatic coupling, solvation models, correlated many particle methods, and molecular properties.

## Materials Science

### CPMD

The Car-Parrinello Molecular Dynamics code is a parallelized plane wave / pseudopotential implementation of Density Functional Theory, particularly designed for ab initio molecular dynamics.

### MEEP

The MIT Electromagnetic Equation Propagation package is a free finite-difference time-domain simulation package to model electromagnetic systems.

### VASP

The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles.

## Fluid Dynamics

### ANSYS Fluent

ANSYS Fluent software enables modeling, simulation, and visualization of flow, turbulence, heat transfer and reactions for industrial applications ranging from air flow over an aircraft wing to combustion in a furnace. Advanced solver technology provides fast, accurate CFD results, flexible moving and deforming meshes and superior parallel scalability. User-defined functions allow the implementation of new user models and extensive customization of existing models. For more information about the application, please go to the ANSYS Fluent web site.

### OpenFOAM

OpenFOAM is an open source CFD package that has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer to solid dynamics and electromagnetics.

### STAR-CCM+

STAR-CCM+ is a comprehensive engineering simulation package from CD-adapco for solving problems involving flow of fluids or solids, heat transfer and stress.

## CAE/Structural mechanics

### COMSOL

The COMSOL Multiphysics simulation environment facilitates all the steps in the modeling process, including defining your geometry, meshing, specifying your physics, solving and visualizing results.

### TAITherm

TAITherm is software for modeling and analyzing heat transfer. It is a thermal simulation tool for comprehensive CAE analysis.

## Biology

### mpiBLAST

mpiBLAST is a freely available, open-source, parallel implementation of NCBI BLAST that can run on distributed computational resources.

### COBRA

(ECOM) The COBRA toolbox for MATLAB and the COBRApy Python modules enable constraint-based modeling and analysis of biochemical networks.

## Weather

### WRF

The Weather Research & Forecasting Model is a next-generation mesoscale numerical weather prediction model designed to serve both operational forecasting and atmospheric research needs. WRF is suitable for a broad spectrum of applications across scales ranging from meters to thousands of kilometers.

## Statistics and Analysis

### Dakota

Dakota is a package from Sandia National Labs for implementing a "Multilevel Parallel Object-Oriented Framework for Design Optimization, Parameter Estimation, Uncertainty Quantification, and Sensitivity Analysis.

### FEniCs

FEniCS is a collection of free, open source software components with the common goal to enable automated solution of differential equations.

**GAMS**

The General Algebraic Modeling System (GAMS) is a high-level modeling system for mathematical programming and optimization.

### Gurobi

Gurobi Optimizer is a solver for mathematical programming.

### Matlab

MATLAB is a package that integrates computation, visualization and programming in an easy-to-use environment where problems and solutions are expressed in familiar mathematical notation.

### R

R is a language and environment for statistical computing and graphics.

## Visualization and Analytics

### VirtualGL/Turbo VNC

Provides remote visualization for OpenGL-based applications. For more information, please go to the VirtualGL/Turbo VNC page.

### ParaView

An open-source, multi-platform data analysis and visualization application.

### Avizo

3D Analysis software for scientific and industrial data.

### VAPOR

VAPOR enables interactive exploration of terascale gridded data sets that are large in both the spatial and temporal domains. Wavelet-based multiresolution data representation permits users to make speed/quality tradeoffs for visual as well as non-visual data exploration tasks.

### IDL

IDL, the Interactive Data Language, is an interactive application used for data analysis, visualization and cross-platform application development.

### VisIt

VisIt is a **free** interactive parallel visualization and graphical analysis tool for viewing scientific data on Unix and PC platforms. VisIt features a robust remote visualization capability, and can be started on a local machine and used to visualize data on a remote compute cluster.