Open Source Software

Submitted by Managers on Fri, 2007-05-11 12:01.

RSS feed for comments on this page: http://imechanica.org/crss/node/1394
This page was started following discussions initiated by Mogadalai Gururajan.

Finite Elements

Some pointers to open source FEM codes
Pre- and Post-Processors

Gmsh
Triangle

Nonlinear Finite Elements

CalculiX
Code_Aster
Impact
OOFEM
Tahoe
Warp3D
FEBio (via)
Linear Finite Elements

Elmer
FEMPACK finite element routines
FETK
OpenFEM
OOF
Extended finite element method codes ; via.

General Computational Mathematical Modeling

FEniCS
GetFEM++
FeaTure

Adaptive Mesh Refinement and Error Estimation

deal.II

Ordinary Differential Equation Solvers

PSIDE

Partial Differential Equation Solvers

ELLPACK
FIPY
JSIM
PDE2D

Meshfree Methods

Element-free Galerkin Matlab routines
Uintah

Open Source CFD and Coupled Codes

CoolFluid
FeatFlow
GETDP
HEDRA
LibMesh
Uintah

Microstructural evolution

Some pointers to open source codes for microstructural evolution
Codes for simulations of dislocations

Molecular Dynamics/Statics and Quantum Chemistry

Biomolecules
- AMBER
- CHARMM ;
- GROMACS,
- NAMD
- NWChem
- ORAC
- TINKER
Polymers, Metals, Gases
- AMBER
- CAMP Open Software project (CAMPOS)
  - Density functional code - dacapo
  - Classical MD and quasticontinuum code - Asap
  - Linear muffin-tin orbital code - LMTO
- CHARMM
- CP2K
- DL_POLY
- GROMACS
- LAMMPS,
- Lennard
- Molecular Modelling ToolKit
- MOSCITO
- NAMD
- NWChem
- ParaDyn
- TINKER

Visualization

SCIRun
AtomEye,
VMD,
RasMol,
Raster3d
MayaVi
Gnuplot

Linear/Nonlinear Algebraic Solvers

PETSC
Amigos
MANPACK

Others

Codes for miscellaneous applications
Some pointers to fast solvers
GNU Scientific library
UbuntuScience
NIST software page
FFTW
Maxima
Sage: Open Source Mathematics Software

Ranked Lists of Free/Commerical Software

Structural Engineering Software Database from BridgeArt.net.

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An old thread on open source finite element code

Submitted by Zhigang Suo on Fri, 2007-05-11 12:43.

Here is an old thread on open source finite element codes: What is status of open source finite element code?

Open source visualization software: SCIRun

Submitted by Biswajit Banerjee on Fri, 2007-05-11 23:14.

Easy and fast visualization of results is an important requirement in scientific computing. We use a set of cuting edge visualization tools from the SCI Institute at Utah on a daily basis. The tool of choice for moderate sized data sets is SCIRun. The SCIRun/BioPSE software is opensource and the latest release can be downloaded from the SCIRun download page. The code is relatively well documented and easy to use and the interface is similar to the now defunct IBM DataExplorer. Use can also explore and download a range of tools from the SCI institute at http://software.sci.utah.edu/ including our code Uintah. You can browse our subversion repository here. Downloading the software requires that you be registered at the SCI institute site. You can contact me if you are interested in the Uintah side of things.
You a watch a video generated in SCIRun below.

Categorizing codes

Submitted by Arun K. Subramaniyan on Sat, 2007-05-12 00:16.

I think the present form of listing codes may soon become unmanageable and too difficult to search. Is there a way in which we can categorize codes (for example like SourceForge) here? It would also help a lot if we can give a brief description of the codes. The description can be easily added once the technique for categorizing is implemented.

Mathematica!

Submitted by Roozbeh Sanaei on Mon, 2007-05-14 17:43.

If you are searching for a really developable code I advise use of Mathematica packages such as IMTEK and ACEFEM because their codes are greatly more readable. Another way is the use of opensource libraries instead of open source applications. For finite elements DEAL.II 5.2.0 has vast documentation.

Re: Mathematica

Submitted by Biswajit Banerjee on Mon, 2007-05-14 18:35.

Dear Roozbeh,

I have taken the liberty to make your post more viewer friendly. Please try to avoid too much capitalization within a sentence. Also life becomes easier for the reader when sentences start with capital letters and each sentence is separated from the next by two spaces.

Mathematica may be useful for certain small applications. However, there are two problems that come to mind:

1) Mathematica is not available for free.

2) It is hard to run big problems with Mathematica based packages and a nightmare to parallelize.

Biswajit

More on open source software

Submitted by Zhigang Suo on Sat, 2007-05-12 12:03.

Dear Guru, Biswajit, Arun:

Thank you very much for getting this page started. I took liberty to modify the title of the page to "Open source software". (see this screen shot) This title was suggetsed by Arun, and looks more explicit than "Open source review" as a button in "Quick guide" on the right side of iMechanica.

Following the suggestion of Arun, I've broken Guru's initial draft into categories. Please feel free to amodify. I think that it is fine for one piece of software to appear under two categories. It might be a good idea to add one sentence to each software to say what it is about. If a thread of discussion on a piece of software appears in iMechanica or elsewhere, we can also add a link of "user forum".

I have also set up Biswajit as a moderator, so that he, too, can edit pages.

If three of you subscribe to the RSS feed of the comments on this pape, when other users give tips on other open source codes or a review of a code, you will be alerted and can update the page.

Everyone: Please help Guru, Arun and Biswajit by adding comments.

A new channel in the header: software

Submitted by Zhigang Suo on Sat, 2007-05-12 23:02.

I've just added a new channel "software" in the header of iMechanica, and relocated a few old posts into this channel. See a screen shot to learn how to post an entry to a channel.

Tahoe from Sandia

Submitted by Biswajit Banerjee on Mon, 2007-05-14 01:48.

Tahoe is a nonlinear finite element code developed at the Sandia National Laboratories. The code contains a large range of tools for the analysis of solids at various length scales. Features include a number of material models, cohesive zone modeling, transferring data to and from a number of formats, etc.

In my opinion, the input format is a bit dated though it conforms to a number of standards. Also, a separate mesh generation tool is needed. The code is reasonably easy to understand but can be a bit difficult to modify without some hand holding.

You can see some of the models that have been implemented in Tahoe at its Doxygen documentation page.

[Update: I have added some more links from http://imechanica.org/node/938.]

Some Useful Keywords

Submitted by Roozbeh Sanaei on Mon, 2007-05-14 17:08.

Public Domain FE Programs

Mesh Generators

FE Visualisation

Public Domain Mathematical Software and Miscellaneous Items

Some Useful Links

Submitted by Roozbeh Sanaei on Mon, 2007-05-14 17:10.

Useful Links:
http://homepage.usask.ca/~ijm451/finite/fe_resources/node15.html
http://www.tecgraf.puc-rio.br/~amiranda/MEF/MEF.html
http://www.scicomp.uni-erlangen.de/archives/SW/diffequ.html http://www.sai.msu.su/sal/B/2/
http://web.ift.uib.no/~jankoc/hfag/femres.txt
http://www.ann.jussieu.fr/free.htm http://www.dmoz.org/Science/Technology/Software_for_Engineering/Finite_Element_Analysis http://www.indiana.edu/~statmath/bysubject/numerics.html#diffeq http://gid.cimne.upc.es/links/index.html

Useful Forums in this regard:
http://imechanica.org/node/470

**Tahoe (Open Source) :
http://tahoe.ca.sandia.gov/
AZTEC: (Open Source):
http://www.cs.sandia.gov/CRF/aztec1.html
AMIGOS: http://www.iue.tuwien.ac.at/phd/radi/node31.html
BROOK: http://frontier.ams.sunysb.edu/frontiercalc2/PDE_Solver/
CEMTool: http://www.cemtool.com/
COMSOL:http://www.comsol.com/
COOLFLUID: http://coolfluidsrv.vki.ac.be/coolfluid/
DOPDEES: http://www.ee.washington.edu/faculty/dunham/
ELLPACK: http://www.cs.purdue.edu/research/cse/pellpack/pellpack.html
ESYS.ESCIPT: (Open Source): http://iservo.edu.au/esys/
FETK: http://www.fetk.org/
FIPY: (open source): http://www.ctcms.nist.gov/fipy/
FLEXPDE: http://www.pdesolutions.com/
GETDP: http://www.geuz.org/getdp/
HAMLAB: http://sts.bwk.tue.nl/hamlab/
HEDRA: http://smirnov.mae.wvu.edu/hedra/index.html
JSIM: http://www.physiome.org/jsim/
MATLAB PDE SOLVER: http://www.mathworks.com/
NUMERICA: http://www.numeritek.com/
PDE2D:(Open Source): http://www.pde2d.com/
PDESOL: http://www.pdesol.com/
PETSC: http://www-unix.mcs.anl.gov/petsc/petsc-as/
PSIDE: http://www.cwi.nl/archive/projects/PSIDE
MANPACK: http://www.scicomp.uni-erlangen.de/archives/SW/SYISDA.html PDEASEDOMAIN: http://www.scientek.com/macsyma/pdmain.htm
PDESOL: http://www.wias-berlin.de/software/pdelib/
OPENFEM: http://www-rocq.inria.fr/OpenFEM/

Molecular Dynamics

Submitted by Roozbeh Sanaei on Mon, 2007-05-14 17:14.

CAMP Open Software project (CAMPOS)
Type: Molecular Dynamics/Force Fields
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.

AMBER
Type: Molecular Dynamics/Force Fields
License: Proprietary
Description: No description

CHARMM
Type: Molecular Dynamics/Force Fields
License: Proprietary
Description: No description

GROMOS
Type: Molecular Dynamics/Force Fields
License: Proprietary
Description: No description

Tight Bending

Submitted by Roozbeh Sanaei on Mon, 2007-05-14 17:15.

Yaehmop
Type: Tight binding
License: GPL
Description: Yet Another extended Huckel Molecular Orbital Package (YAeHMOP) was developed by Greg Landrum whilest a graduate student in the research group of Professor Roald Hoffmann at Cornell University. YAeHMOP is intended to be an easy to use, transparent, extended Huckel calculation and visualization package which can perform calculations on both molecular and extended materials in 1,2, or 3 dimensions.

DensEl
Type: Tight binding
License: Proprietary
Description:

ParaDens
Type: Tight binding
License: Proprietary
Description:

Quantom Mechanics

Submitted by Roozbeh Sanaei on Mon, 2007-05-14 17:20.

2D-Numerical
Type:
Quantum Chemistry: Hartree Fock/MP/CC/CI
License:
GPL
Description: A numerical Hartree-Fock program for diatomic
molecules.
Ghemical
Type:
Quantum Chemistry: Hartree Fock/MP/CC/CI
License:
GPL
Description: A molecular modelling software package with nice
3D-visualization tools.
MPQC
Type:
Quantum Chemistry: Hartree Fock/MP/CC/CI
License:
GPL
Description: MPQC is the Massively Parallel Quantum Chemistry
Program.
PyQuante
Type:
Quantum Chemistry: Hartree Fock/MP/CC/CI
License:
GPL
Description: PyQuante is a suite of programs for writing quantum
chemistry software. The program is written in the Python programming language,
but has many "rate-determining" modules also written in C for speed. The
resulting code is not nearly as fast as Jaguar, Gaussian, or GAMESS, but the
resulting code is much easier to understand and modify.
GAMESS
Type:
Quantum Chemistry: Hartree Fock/MP/CC/CI
License:
Proprietary
Description:
GAMESS-UK
Type:
Quantum Chemistry: Hartree Fock/MP/CC/CI
License:
Proprietary
Description:
GAUSSIAN
Type: Quantum
Chemistry: Hartree Fock/MP/CC/CI
License:
Proprietary
Description:
JAGUAR
Type:
Quantum Chemistry: Hartree Fock/MP/CC/CI
License:
Proprietary
Description:
MOPAC
Type:
Quantum Chemistry: Hartree Fock/MP/CC/CI
License:
Proprietary
Description:

Density Functional

Submitted by Roozbeh Sanaei on Mon, 2007-05-14 17:21.

ABINIT
Type: Density
Functional
License: GPL
Description:
CAMP Open Software project
(CAMPOS)
Type: Density Functional
License:
GPL
Description:
octopus
Type:
Density Functional
License: GPL
Description: Octopus is
a program aimed at the ab initio virtual experimentation on a hopefully ever
increasing range of systems types. Its main characteristics are:
- Electrons are describe quantum-mechanically within the Density-Functional
  Theory (DFT), in its time-dependent form (TDDFT) when doing simulations in time.
  Nuclei are described classically as point particles.
- Electron-nucleus interaction is described within the Pseudopotential
  approximation.
PWSCF
Type: Density
Functional
License: GPL
Description:
SPINOR
Type:
Density Functional
License: GPL
Description: The ab
initio Spinor Project is a scientific code project based on density functional
theory (DFT) within the ab initio pseudopotential frame work. The code
implements the fundamental Kohn-Sham functions in form of two-component
spinors.
CARPAR
Type:
Density Functional
License: Freeware
Description: The
tutorial version of a Car-Parrinello code
CP2K
Type:
Density Functional
License: Freeware
Description:
DoD-Planewave
Type:
Density Functional
License: Freeware
Description: A
General Scalable Density Functional Code
FHI96MD
Type:
Density Functional
License: Freeware
Description: The
FHI96MD program is an efficient code to perform molecular dynamics simulations
and total-energy calculations for molecules, perfect crystals, defects,
surfaces, interfaces and dislocations in crystals for materials as different as
semiconductors, simple and transition metals, insulators, etc. The program
employs density-functional theory, first-principles pseudopotentials, and a
plane-wave basis set.
PWPAW
Type:
Density Functional
License: Freeware
Description: A
Projector Augmented Wave (PAW) code for electronic structure calculations.
PartII: pwpaw for periodic solids in a plane wave basis. Computer Physics
Communications 135, 348-376 (2001)

Pseudopotential/Pseudoprojector generators

Submitted by Roozbeh Sanaei on Mon, 2007-05-14 17:22.

Vanderbilt Ultra-Soft
Pseudopotential
Type: Pseudopotential/Pseudoprojector
generators
License: GPL
Description: The 'UltraSoft
PseudoPotential' (USPP) generation code from the group of David Vanderbilt at
Rutgers University.
AtomPAW
Type:
Pseudopotential/Pseudoprojector generators
License:
Freeware
Description: A Projector Augmented Wave (PAW) code for
electronic structure calculations.
Part I: atompaw for generating
atom-centered functions Computer Physics Communications 135, 329-347
(2001)
FHI98PP
Type:
Pseudopotential/Pseudoprojector generators
License:
Freeware
Description: The package fhi98PP allows one to
- Generate norm-conserving pseudopotentials of the Hammann and
  Troullier-Martins types, employing common parameterizations of the local-density
  approximation and the generalized gradient approximation for exchange and
  correlation.
- Check the transferability of one's pseudopotentials, in particular to search
  for unphysical ghost states of their fully separable (Kleinman-Bylander)
  representation.
Jose-Luis Martin's
pseudopotential code
Type: Pseudopotential/Pseudoprojector
generators
License: Freeware
Description: No
description

Is there any reliable ranking for open source programs?

Submitted by Roozbeh Sanaei on Mon, 2007-05-14 17:36.

Working with an open source program takes a lot time. Choosing a nice open source program is really important. But i did'nt find any reliable ranking for open source programs. According to citation and availability I have found general purpose programs DEAL.II, ALBERT, GROMACS, and PETSC better than others. But for a special purpose it is evident that one program can be great.

For example Sandia's TAHOE as mentioned in the above have great tools for non-linear models and atomistic-continuum bridging. But it is not good choice for example in electromagnetism! And OPENFOAM was great for modelling supercavitation. Is there any one who has any information about QM/MM simulating using GROMACS?

Re: Reliable ranking of open source programs

Submitted by Biswajit Banerjee on Mon, 2007-05-14 18:47.

Roozbeh,

I've edited out some of the capitalization from your comment. Please try to avoid that in the future because that too many capital letters make the comment hard to read.

Your lists of software are impressive. The ranking of a particular software depends on the particular use it is intended for. General purpose software is useful for a larger group of people than very specialized software. I would rank those higher. Ease of use and modification should also play a role in the ranking of software.

One way you could help at this stage is to give some details of the softwares that you have listed. You can restrict yourself to those that you have actually used and know the strengths and weaknesses of. You could also rank these yourself and then we can list these on the main page.

Biswajit

Should iMechanica regularly review software?

Submitted by Zhigang Suo on Tue, 2007-05-15 21:45.

The large number of open-source software listed by Roozbeh seems to raise a question: Should iMechanica regularly review software?

One possible mode of operation can be similar to the jClub. A few enthusiastic users form a council, which then invites other individuals to review software. Each month, say, an individual selects one theme, or just a piece of software, writes what he knows about the software. What does the software do? Which other software are competitors? Who are the developers? The software can be either open-source or closed-source, so long as it is likely to be useful to mechanicians. The review may be placed as the top post in the Channel "software" for the month, or may be even placed on the top of the front page for the first week.

Other experienced users can add their experiences with the software, or ask questions. Individual software may have its own web site and online community. What iMechanica may offer is a pointer to that community, as well as a comparision of various similar software packages.

Is this a useful thing to do for iMechanica?

Yes! Software review is a great idea

Submitted by Mogadalai Gururajan on Tue, 2007-05-15 22:24.

Dear prof. Suo,

I think it is a great idea--for several reasons.

First is the value addition--there are so many codes that the end user would really like to have an idea as to which one she wants to use, without proceeding by trial and error;
Second is the fact that an experienced user, with a short example, can make the process of using the software easier--for example, a sample code as to how FFTW can be used and/or optimised for solving PDEs would make it much easier for beginners--I learnt by looking at such template code, and modifying it for my purposes. It works great!; and,
Third (even though not the primary benefit), such reviews, if use example problems from different areas of research might also serve the users to have hands on experience--thus, iMechanica will be serving as a forum for teaching each other some part of mechanics using the software as a tool.

I can also see that in some cases it might lead to collaborations, and/or improvement of the existing software--at the minimum, it will at least make the users aware of any problems or grey areas that mihgt be lurking behind the black box. Hence, I guess an nClub (for numerical Club) would be very welcome!

Reviewing software is a welcome addition

Submitted by Arun K. Subramaniyan on Wed, 2007-05-16 01:27.

Dear Prof. Suo,

I also think that reviewing software in a forum similar to JClub is a very good idea. It is certainly a very unique addition to iMechanica. I like Guru's suggestion for an apt title (nClub) as well.

Software articles

Submitted by Bill Greene on Wed, 2007-05-16 15:05.

Zhigang,

As someone whose primary interest is computational mechanics and who
works in the commercial software industry, I would welcome more
discussions of software. I'm not exactly sure what form this should take or
how to encourage it, though.

As you can imagine, it is extremely difficult to write a broad "review" of
a general purpose analysis package. It becomes even more difficult if
more than one code is involved; the author has to be something of an
expert in all packages. These kind of reviews typically degenerate into
a Consumer Report -style checkbox format that I don't think is
particularly useful.

What seems more useful to me would be articles that focus on a user's
experience with a particular problem or small class of problems.
One source of these might be student projects
from an advanced FEA or applied mechanics class. Could be
an opportunity for the students to share some useful insights with a larger
audience. These users may not, in general, be "experts" with the software
but, by the time they finish the project, they may have become experts
in a specific area of the software.

I haven't followed the jClub procedure that carefully but I can imagine
something like that would work here. Perhaps interested authors could
submit abstracts, one of which would be selected each month for the
feature article. I think some sort of editorial control might be necessary
to keep commercial developers (like me ) from turning these articles into
thinly-veiled advertisements.

Bill

Open Source Software

Submitted by Biswajit Banerjee on Mon, 2007-06-25 21:26.

I have added the possibility of having links to expert opinions and ratings in the open source software page. Please add comments rating the software that you have used. For now the maximum number of allowable smileys is five. I'll average your ratings and post a rounded number of smileys in the main page.

categorized information

Submitted by Roozbeh Sanaei on Wed, 2007-05-16 10:06.

i think most information and details about a software may be find in it's
web page.

of course, an experienced user, with a short example or short comment can
make the process of using the software more easier. but i think one of primary
difficulties for researchers is to find a suitable software for special purpose.
For example, What is the main advantage and disadvatages of DEAL.II on ALBERT.
both of them are developed for solve PDE's using Adaptive Finite Element method.
but which of them is better for a special work. Sometimes, Using a suitable
software to do a specific task make it more simpler. it think categorization of
existent softwares is a really good manner to help investiagtors to do so. in
addition, in the case of giving infomation about a software it must be done in a
categorized way. questions and answers about open source softwares are found in
the internet very much but finding a specific answer for a special questions
some times is harder than try and error. because this information are unsorted.
this problem may be handled by sort answers and questions of users. overally i
think it is very good idea. but categorization of information is very very
important too.

iMechanica

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Open Source Software

An old thread on open source finite element code

Open source visualization software: SCIRun

Categorizing codes

Mathematica!

Re: Mathematica

More on open source software

A new channel in the header: software

Tahoe from Sandia

Some Useful Keywords

Some Useful Links

Molecular Dynamics

Tight Bending

Quantom Mechanics

Density Functional

Pseudopotential/Pseudoprojector generators

Is there any reliable ranking for open source programs?

Re: Reliable ranking of open source programs

Should iMechanica regularly review software?

Yes! Software review is a great idea

Reviewing software is a welcome addition

Software articles

Open Source Software

categorized information