Revision of Open Source Software from Fri, 2007-06-08 11:52

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Finite element methods

Open Source CFD and Coupled Codes

Microstructural evolution

Biomolecules

Molecules (Statics and Dynamics)

  • CAMP Open Software project (CAMPOS)
    Type: Molecular Dynamics/Force Fields (via )
    License: GPL
    Description: The CAMPOS project consists of several atomistic
    simulation tools and an environment for setting up atomistic
    calculations and visualizations, written in Python. Currently the
    atomistic simulation tools include dacapo, a density functional
    program, Asap, a set of python classes, that can be used for doing
    atomistic simulations of systems containing up to millions of atoms and
    a linear muffin-tin orbital (LMTO) program. Asap is a tool for
    classical molecular dynamics simulations. The current version supports
    parallel simulations on e.g. clusters of workstations. It scales well
    up to at least a few hundred workstations even with 100MB/s ethernet
    communication. The interatomic forces are described in the Effective
    Medium Theory (EMT). The modular structure allows for easy
    implementation of other interatomic potentials, without having to worry
    about the subtleties of parallel programming. Asap includes modules for
    quasicontinuum (QC) simulations. In regions of space where stress and
    strain fields are slowly varying, the atoms are replaced with a mesh of
    representative atoms, leading to a dramatical reduction in the number
    of degrees of freedom, while maintaining atomic-scale resolutions where
    that is required. The QC part of Asap is not yet running on parallel
    computers.
     
  • GROMACS
    Type: Molecular Dynamics/Force Fields
    License: GPL
    Description: 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 and lipids 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.
     
  • Lennard
    Type: Molecular Dynamics/Force Fields
    License: GPL
    Description: Noble Gas Simulator.
     
  • Molecular Modelling ToolKit
    Type: Molecular Dynamics/Force Fields
    License: GPL
    Description: The Molecular Modelling Toolkit (MMTK) is an Open
    Source program library for molecular simulation applications. In
    addition to providing ready-to-use implementations of standard
    algorithms, MMTK serves as a code basis that can be easily extended and
    modified to deal with standard and non-standard problems in molecular
    simulations.
     
  • MOSCITO
    Type: Molecular Dynamics/Force Fields
    License: GPL
    Description: MOSCITO is designed for molecular dynamics
    simulations of condensed phase systems defined by classical molecular
    mechanics force-fields such as AMBER, OPLS, CHARMM and GROMOS.
     
  • ORAC
    Type: Molecular Dynamics/Force Fields
    License: GPL
    Description: ORAC is a program for running classical
    simulations of biomolecules. Simulations can be carried out in the NVE,
    NPT, NHP, and NVT thermodynamic ensembles.
     
  • CP2K
    Type: Molecular Dynamics/Force Fields
    License: Freeware
    Description: A program package to do atomistic and molecular
    simulations of solid state, liquid, molecular and biological systems.
    The methods included range from first principles ab initio density
    functional methods to parametrised, classical pair- and many-body
    potentials.

Visualization

  • SCIRun (via) -- Scientific Visualization code from University of Utah.
  • AtomEye,  
  • VMD
  • RasMol
  • Raster3d 
  • MayaVi -- A scientific data visualization tool kit written in Python
  • Gnuplot -- A copyrighted, but freely distributed plotting software

Linear/Nonlinear Algebraic Solvers 

Ordinary Differential Equation Solvers 

Partial Differential Equation Solvers 

Others

  • Codes for miscellaneous applications -- for rotations, Mohr's circles, visualization, elastic constants calculation etc; via .
  • Some pointers to fast solvers
  • GNU Scientific library -- A collection of C/C++ library for a range of numerical tasks, and is a must-visit site for anybody who is even remotely interested in using computers for scientific calculations. The GSL homepage also lists related packages, extensions/applications and wrappers for other languages.
  • UbuntuScience -- A comprehensive collection of software that can be run on Linux
  • NIST software page -- Among other things, the software listed include those for the study of multizone airflow, structure and properties of cement based materials, scientific visualization, statistical analysis, non-linear modelling, a guide to the available mathematical software (cross-indexed),  and smoke plume modelling.
  • FFTW   -- a C subroutine library for  discrete Fast Fourier Transforms (FFT); benchmarked and portable, a choice program for FFTs
  • Maxima -- A GPL computer algebra system implemented in LISP that can do symbolic, and numeric computations (and, plotting too). Among other things, the code can do symbolic manipulations on tensors.

Here are some links to open source codes/software available on the net; all this information is collected from different posts at iMechanica. It is quite possible that we missed some, and some that are listed are not open source. If so, please feel free to edit the post or leave a comment with relevant links so that we can edit the post.

If you write a post or comment about some codes/software or if you notice one while you are reading the posts at iMechanica, please leave a note in the comments or include the information in the listing below.

If you have some code you would like to share with mechanicians, write a post in your blog and leave a comment here, so that we can update the repository database. 

We believe, over a period, we might be able to build a very authorotative and useful repository of codes here, so that this post becomes a one-stop shop for any of your code needs.