Software and Tools

[Computational Structural Analysis][Quantum Chemistry] [Semiempirical][Molecular Mechanics / Dynamics] [Crystallography and Materials Science] [Computational Fluid Dynamics] [Math and Statistics] [Compilers & Programming] [Visualization] [Supported Operating Systems] [Bioinformatics] [Other Simulations]


Computational Structural Analysis


ANSYS

A suite of programs for structural mechanics. *

ABAQUS

Finite element analysis program for structural mechanics. Both Abaqus/Standard and Abaqus/Explicit are available. *

Hyperworks

Graphic interface for use with engineering software packages. *


[Back to Top of Page]


Quantum Chemistry


ADF

ADF (Amsterdam Density Functional) is software for first-principles electronic structure calculations. ADF is used by academic and industrial researchers in such diverse fields as pharmacochemistry and materials science. It is particularly popular in the research areas of homogeneous and heterogeneous catalysis, inorganic chemistry, heavy element chemistry, various types of spectroscopy, and biochemistry. *

CPMD

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

GAUSSIAN 03

The pre-eminent ab initio quantum mechanics package. Gaussian has a very large range of quantum mechanical methods.

JAGUAR

High performance quantum mechanics package. Jaguar scales more favorably to large numbers of atoms than many other ab initio codes. *

GAMESS

The General Atomic and Molecular Electronic Structure System is an ab initio quantum chemistry code.

GAMESSPLUS

An extended version of GAMESS, which includes solvation effects.

NWChem

A highly parallelized package for quantum chemistry and molecular dynamics.

POLYRATE

POLYRATE computes chemical reaction rates using variational or conventional transition state theory. POLYRATE is designed to compute additional information using data generated by other programs as its input. (e.g., the results computed by GAMESS or Gaussian can be used as the input to POLYRATE).

Quantum-ESPRESSO

The Quantum-ESPRESSO package contains software for Density-Functional Theory calculations using a Plane-Wave basis sets and pseudopotentials.

LmtART

The program LmtART is an implementation of full-potential linear-muffin-tin-orbital method for electronic-structure calculations. It is designed to perform band structure, total energy and force calculations within the methods of density functional theory (DFT).

PSI3

The PSI3 suite of quantum chemical programs is designed for efficient, high-accuracy calculations of properties of small to medium-sized molecules. The package's current capabilities include a variety of Hartree-Fock, coupled cluster, complete-active-space self-consistent-field, and multi-reference configuration interaction models. Molecular point-group symmetry is utilized throughout to maximize efficiency.

ORCA

ORCA is a flexible, reasonably 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 correlated ab initio methods. It can also treat environmental and relativistic effects. *

GAUSSRATE

Allows reaction rates to be computed using the Gaussian software package.

MULTILEVEL

Multilevel is a program for doing dual-level and multi-level computations. *

Dalton

Dalton is a powerful molecular electronic structure program, with an extensive functional for the calculation of molecular properties at the HF, DFT, MCSCF, and CC levels of theory..

ACES II

ACES II (= Advanced Concepts in Electronic Structure) is a series of programs for performing high-level quantum chemical ab initio calculations. Its major strength is the accurate calculation of atomic and molecular energies as well as properties using "many-body" techniques such as many-body perturbation theory (MBPT) and, in particular coupled-cluster techniques to treat electron correlation. *

[Back to Top of Page]


Semiempirical


MOPAC

MOPAC is a general purpose, semi-empirical molecular orbital program for the study of chemical reactions involving molecules, proteins, ions, and linear polymers.

AMSOL

Semiempirical chemistry code designed to model molecules in solution. *


[Back to Top of Page]


Molecular Mechanics / Dynamics


Autodock

AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.

GROMACS

The GROMACS developers claim that it is the world's fastest molecular dynamics program.

GROMOS 96

A molecular mechanics and dynamics program for simulating molecules, liquids and biomolecules. NWChem A highly parallelized package for quantum chemistry and molecular dynamics. *

NAMD

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD uses the molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM, and X-PLOR.

Tinker

The TINKER molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers.

GULP

GULP is a program for performing a variety of types of simulation on materials using boundary conditions of 0-D (molecules and clusters), 1-D (polymers), 2-D (surfaces, slabs and grain boundaries), or 3-D (periodic solids). The focus of the code is on analytical solutions, through the use of lattice dynamics, where possible, rather than on molecular dynamics.*

Amber

Amber stands for "Assisted Model Building with Energy Refinement". It is a suite of packages for running molecular dynamics and mechanics simulations.*



[Back to Top of Page]


Crystallography and Materials Science


Crystal

A program for ab initio and density functional theory calculations on crystals.

CCP4

Crystallography & NMR structure determination package. *

CNS

Crystallography & NMR structure determination package. *

X-PLOR

Crystallography & NMR structure determination package.*

ABINIT

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 basis.

[Back to Top of Page]


Computational Fluid Dynamics


FIDAP
FIDAP is a computational fluid dynamics (CFD) package that analyzes fluid flow including heat and mass transfer. It includes comprehensive pre- and post-processing capabilities and a flexible and powerful solver. *
FLUENT

FLUENT is a general purpose finite volume code useful for modeling complex flows ranging from incompressible to highly compressible (up to Mach 10).  Included models can accurately predict laminar, transitional and turbulent flows, various modes of heat transfer, chemical reaction, and multiphase flows.  Both structured and unstructured meshes are supported. *

GAMBIT

GAMBIT is available on local workstations as a pre-processor/grid builder for FLUENT and FIDAP. It supports structured and unstructured meshes and can import ACIS and IGES/CAD geometries.  Some low level boundary conditions can also be applied within GAMBIT. *

MM5

A fluid dynamics program for modeling weather patterns.

CFD-ACE+ and CFD-FASTRAN

CFD-ACE+ is an advanced CFD & multiphysics software package. It enables coupled simulations of fluid, thermal, chemical, biological, electrical and mechanical phenomena. CFD-FASTRAN is a leading commercial CFD software for aerodynamic and aerothermodynamic applications. It employs state-of-the-art multiple moving body capability for simulating most complex aerospace problems including missile launch, maneuvering and staging, and aircraft flight dynamics and store separation. *

INS2D and INS3D

The INS2D/INS3D codes solve the incompressible Navier-Stokes equations in two-dimensional/three-dimensional generalized coordinates for both steady-state and time varying flow. The equations are formulated into a hyperbolic set of PDE using the method of artificial compressibility. The convective terms are differenced using an upwind biased flux-difference splitting. The equations are solved using an implicit line-relaxation scheme. The code is written for single or multiple-zone calculations. It can utilize either pointwise continious zonal interfaces, or random overlapped zonal interfaces if a PEGASUS interpolation database is supplied. The flow solver contains pre-coded boundary conditions for slip and noslip walls, symmetry planes, inflow and outflow boundaries, and far-field boundaries.

WRF

A fluid dynamics program for modeling weather patterns.


[Back to Top of Page]


Math and Statistics



deal.II

deal.II is a C++ program library targeted at the computational solution of partial differential equations using adaptive finite elements.

IMSL

The IMSL Libraries are a comprehensive resource of more than 900 FORTRAN mathematical and statistical subroutines for scientists, engineers, and mathematicians.

Trilinos

The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems. A unique design feature of Trilinos is its focus on packages.

METIS

METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices.

PDE2D

PDE2D solves quite general nonlinear, time-dependent, steady-state, and eigenvalue systems of partial differential equations.

PETSc

PETSc is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations.

SLATEC

SLATEC is a math library that supports such calculations as: arithmetic, error analysis; elementary and special functions; elementary vector operations; solutions of systems of linear equations; and much more.

MKL

A thread-safe math library from Intel.

f2cblaslapack

Fortran-to-C blas & lapack libraries.

SCSL

Math library from SGI, which uses mpt parallelization.

Octave

A high-level interactive language for numerical computations. CLICK HERE for compatability information.

ACML

The AMD Core Math Library (ACML) incorporates BLAS, LAPACK and FFT routines, which are designed to obtain excellent performance running on AMD platforms.

R

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

GAP

Groups, Algorithms, Programming - A system for computational discrete algebra.

Lapack++

LAPACK++ is a library for high performance linear algebra computations.


[Back to Top of Page]


Compilers & Programming


OpenMP

OpenMP is a means for creating shared memory parallel programs through the use of compiler directives and OpenMP capable compilers.

GASNet

GASNet is a language-independent, low-level networking layer that provides network-independent, high-performance communication primitives tailored for implementing parallel global address space SPMD languages.

Unified Parallel C

Unified Parallel C (UPC) is an extension of the C programming language designed for high performance computing on large-scale parallel machines.

Fortran 77 & Fortran 90

Fortran compilers from GNU and Intel.

MPI

Message passing libraries are available for messaging over NUMA-link and infiniband connections.

Assembler

GNU assembler.

C/C++

C and C++ compilers from GNU and Intel.

Perl, python, awk, tk, tcl

Unix scripting languages.

gprof

GNU code profiling tool.

Blassic

Blassic is a classic Basic interpreter. The line numbers are mandatory, and it has PEEK & POKE. The main goal is to execute programs written in old interpreters, even those that use peculiar control flow constructs or automodifiable code. However, it can be used as a scripting language, and has some not-so-classic instructions. It has graphics modes that are compatible with some classic systems and user defined.


[Back to Top of Page]


Visualization


NCAR Graphics

A set of FORTRAN library routines for generating graphics from a user application.

gnuplot

A portable command-line driven interactive datafile (text or binary) and function plotting utility.

Grace

A WYSIWYG 2D plotting tool for the X Window system.

VMD

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.

[Back to Top of Page]


Supported Operating Systems


Linux
 

[Back to Top of Page]


Bioinformatics


MrBayes

MrBayes is a program for the Bayesian estimation of phylogeny.

Karma

Karma is a high speed aligner for mapping FASTQ reads to a reference genome.

TopHat

TopHat is a splice junction mapper for short RNA-Seq reads.

PHASE

The program PHASE implements methods for estimating haplotypes from population genotype data.

Map

Maq stands for Mapping and Assembly with Quality. It builds an assembly by mapping short reads to reference sequences. Maq was previously known as mapass2.

Bowtie

Bowtie is an ultrafast, memory-efficient short read aligner.

Velvet

Velvet is a sequence assembler for very short reads.

SHRiMP

SHRiMP stands for SHort Read Mapping Package. SHRiMP is a software package for aligning genomic reads against a target genome.

UMFPACK

UMFPACK is a set of routines for solving sparse linear systems via LU factorization.

mpiBLAST

A parallel version of NCBI BLAST.

NCBI ToolBox

A suite of bioinformatics utilities, including NCBI BLAST.

Twinscan

Twinscan finds genes in a "target" genomic sequence by simultaneously maximizing the probability of the gene structure in the target and the evolutionary conservation dervied from "informant" genomic sequences.

WU-Blast *

A program for searching databases of DNA and protien sequences.

RepeatMasker *

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.

ClustalW

A general purpose multiple sequence alignment program for DNA or proteins.

[Back to Top of Page]


Other Simulations


NS-2

Ns is a discrete event simulator targeted at networking research. Ns provides substantial support for simulation of TCP, routing, and multicast protocols over wired and wireless (local and satellite) networks.

[Back to Top of Page]


* Commerical users and academic researchers doing work under contract to commercial customers must pay an additional fee for the use of this software.