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• This page was started following discussions initiated by Mogadalai Gururajan.

Finite element methods

• Some pointers to open source FEM codes
• 1D and 2D Element-free Galerkin (EFG) method Matlab routines ; via .
• FEMPACK finite element routines -- suite of Matlab routines for PDEs; via .
• Extended finite element method codes ; via .
• Tahoe -- Nonlinear Finite Element and Mesh Free software from Sandia (see comment for more on Tahoe).
• OpenFEM
• FETK

Open Source CFD and Coupled Codes

• CoolFluid
• HEDRA
• GETDP

Microstructural evolution

• Some pointers to open source codes for microstructural evolution
• Codes for simulations of dislocations ; via .

Biomolecules

• CHARMM ; 
• TINKER ; via . 
• NAMD,
• AMBER, 
• GROMACS, 
• NWChem

Molecules (Statics and Dynamics)

• LAMMPS,  
• DL_POLY,  
• NAMD,
• AMBER, 
• GROMACS, 
• NWChem,  
• CHARMM,  
• ParaDyn , 
• TINKER(serial)

• 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 

• PETSC
• Amigos
• MANPACK

Ordinary Differential Equation Solvers 

• PSIDE

Partial Differential Equation Solvers 

• ELLPACK
• FIPY
• JSIM
• PDE2D

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.