iMechanica - Open Source Software - Comments

Blender, TetGen, ParaView, and MechSys

pedroso — Tue, 28 Jun 2011 03:52:38 -0400

Hi All,

I would like to suggest Blender as a drawing tool, TetGen as a mesh generator, and ParaView as a visualization tool. After the geometry is defined with Blender, someone may use a Python script: tetgen_export.py to generate the input files of TetGen. Additionally, for C++ developers, someone may use the libraries available in MechSys in order to, or write his/her own FE program or use a 3D soil-water unsaturated coupled FE program also availabe in that site.

Regards.

SOFEA open-source Matlab finite element tool kit

Petr Krysl — Tue, 13 Nov 2007 18:47:53 -0500

I saw on this page some discussion of Matlab versus FORTRAN versus C++. Perhaps you'll pardon my plug for my open-source Matlab finite element toolkit, SOFEA. I hope you'll check it out (http://hogwarts.ucsd.edu/~pkrysl/sofea).

Cheers,

Petr

Tochnog program (from

osman f. buyukisik — Sat, 29 Sep 2007 16:06:34 -0400

Tochnog program (from sourceforege) is especially suited for consolidation and geotech work. It is kinda old and is not supported anymore, Still compiles ok. The author has chosen to support it commercially.

HTH

-osman

XFEM Deal.ii?

biplab — Fri, 28 Sep 2007 12:58:27 -0400

Couple of months back I had the same question regarding the available FEM libraries. I had a quick glance through the Deal-II feature set. It appeared no-one has used Deal-II so far for XFEM. (Please correct me if I'm wrong).

You may find a comparison of what Deal-II can't do from the following link.

http://home.gna.org/getfem/getfem_faq.html

I don't have any test results to prove their claims. But for sure, one can write a XFEM program with GetFem++ (Though I posted some negative opinion about them). They do provide a sample code to analyse a XFEM problem, too.

The same is true for meshfree methods, too.

OpenXFEM++ sourceforge

Stephane Bordas — Wed, 26 Sep 2007 07:21:42 -0400

Hi Biplab,

It is great to see your interest. OpenXFEM++ is not yet released on an open source term, but this was our next step. We are also trying to couple it with OOFEM, and then, perhaps it can be released that way. My trouble was that I did not know how many people would be interested in contributing, and thought it would not make much sense for such a "simple" code to be released this way. However, I do not know if this is true or not. I could use a lot of help to further develop the code (for instance, make it more efficient and parallel).

Thank you for your suggestions, let's keep this flowing stephane . bordas @ gmail . com

Dr Stephane Bordas

http://people.civil.gla.ac.uk/~bordas

Re: OpenXFEM++ fracture and Ph.D's

biplab — Wed, 26 Sep 2007 05:16:28 -0400

Thank you very much for your reply and your suggestion.

I went through the documentation of OpenXFEM++ and also it's code embedded in it. The code is quite readable and thanks for making it that way.

But is there any plan to release it through some open source software publishing platform?? I mean to say like using SourceForge.Net or Berlios (This is based in Germany). That would help other members to contribute code to the project.

Though I have some complaints against Berlios. I'm an active developer of Code::Blocks (An Open-source Cross-Platform IDE). We use Berlios as our code publishing platform. It often remains inaccessible to Non-EU developers (like me).

I wish I could contribute to your project. Definitely if I use OpenXFEM++ in my future development, I'll post improvements, if any.

Thanks,

Biplab

http://biplab.in

Re: Open source libraries

biplab — Wed, 26 Sep 2007 04:50:31 -0400

Thank you for your reply.

I do agree with you with this trend among Open-Source developers. I do not blame them as most of them often develop it at their free time and it's the code that matters to most of them. But most of them follow certain rules while naming the variables and different classes so that the other members are able to decipher the code.

I gave one example of an unusual GetFem++ class name. Honestly I appreciate their hard work. But I'd request them to make the code more readable.

PS: I do actively contribute in Open-Source Development. I'm an active developer of an Open-Source Cross-Platform IDE (Code::Blocks, http://forums.codeblocks.org/index.php/board,20.0.html)

Re: Open source libraries

Dan Cojocaru — Tue, 25 Sep 2007 10:21:58 -0400

:-) People working for open source projects are usually really passionate about their work but
... programmers/developers don't like to write code documentation if they do not have to.

I think it is rather the rule that open source codes come at best with automatically generated documentation.

XFEM Deal.ii?

Stephane Bordas — Tue, 25 Sep 2007 07:14:59 -0400

Hi,

I think that two tests could be performed to ensure a library is generic enough:

1) code partition of unity enrichmen, XFEM, GFEM, PUM, PUFEM...

2) code meshfree methods

Any comments as to the possibilities of these codes for such endeavours? By experience, this is not trivial, with any library.

Dr Stephane Bordas

http://people.civil.gla.ac.uk/~bordas

OpenXFEM++ fracture and Ph.D's

Stephane Bordas — Tue, 25 Sep 2007 04:51:05 -0400

Hi!

Thanks for using our code. Nguyen Vinh Phu is the author of this matlab code. We also developed an open source XFEM code for any problem, and we are planning to introduce it into OOFEM, but we need people to help us with this. If anyone is interested, it would be a pleasure to introduce OpenXFEM++ into OOFEM with them, I think that this will be a nice step for the community.

I advise the use of gmsh for pre and post-pro, it is a really nice tool.

All the best form Glasgow,

Stephane

PS: I have three Ph.D. theses available in fracture mechanics.

Dr Stephane Bordas

http://people.civil.gla.ac.uk/~bordas

Re: Open-source libraries

biplab — Mon, 24 Sep 2007 03:41:36 -0400

Thank you for your reply.

I agree with you completely that there is no substitute of coding these things by myself. I intend to do the same after I familiarise with the xfem analysis procedures.

At the moment I'm using a xfem code published by Dr. Stéphane BORDAS (http://www.civil.gla.ac.uk/~bordas/codes/xfemMatlab/xfemMatlabCode.rar). This one has given me a good insight on how to proceed.

But I have few queries related to the input / output format that I should use while writing my own program.

1) Which input format do you suggest me to use in my program so that I can extract the mesh & other related informations from a commercial FEA package? I have access to ANSYS and ABAQUS.

2) Which output format do you recommend? During the testing of GetFem++ sample programs I encounterd files with VTK and OpenDX format. I came to know that VTK file formats doesn't support multiple meshes in a single file. OpenDX file can solve this. Kindly post if you know any alternative file formats that can be used.

Thanks in advance.

Biplab

Re: Open-source libraries

N. Sukumar — Thu, 20 Sep 2007 23:36:34 -0400

Yes, I can empathize with you. With C++, one can get carried away with too much ``templatizing'' and/or making it very general (differential forms for constitutive laws and for bilinear forms, etc.). Such a need might not be necessary, even though it is mathematically aesthetic and elegant. Often, if the package is focused on just a few specific goals, then it is easier to meet the demands of readability, speed, and user-friendliness. That said, if a library does provide X and Y functionalities, then it might not meet the needs and/or expectations of those who also wan't Z_1, Z_2, . . , Z_n. Overall, linear solvers are a good open-source library example that are mature and used by many; the service they provide is just one (solving Ax = b for different forms of A). To expect such from open-source fem codes is a tad unreasonable. For the purpose of learning, understanding (pros and cons), and appreciating the subtleties of any computational model, there is no substitute to coding the key ingredients of the same by oneself.

Open source libraries with mathematical aspect

biplab — Thu, 20 Sep 2007 15:15:25 -0400

The mathematical point of view is a good aspect as you've explained. But some of these Open-source packages are so cryptic, it raises a question about their goal.

My research area is in xFEM. For the past couple of months I was suffering with one such package. I started with GetFem++. Here is the horrible experience that I faced.

1) Initially it's sample were exporting garbage vtk output files (which were not recognised by MayaVi or VisIt). Later I found that I should export the VTK files in ASCII text.

2) The documentation is insufficient. I should say it's bare minimum.

3) The GetFem++ library uses horrible naming scheme. E.g., to specify boundary conditions, the class names starts with mdbrick_.

4) The source code has very little comments. On top of that it uses a large number of templates. This make the code quite unreadable.

E.g., the following code can be compiled. But if such code is present in over 100s of files, it's really difficult to understand what's going on.

#include<iostream>

using namespace std;int main(){cout<<"Hello World"<<endl;return 0;}

I have fair knowledge of programming. But till date I couldn't figure out how to write a basic xfem analysis program with it.

An open-source source without proper documenation is as good as an closed one. So even if an average user, like me, wishes to use their goodness and contribute by extending it, there are still large number of hurdles to cross.

In my honest opinion, if these packages sacrifice a little bit of Software Engineering and be more user-friendly, we may see some good packages coming up. Otherwise they will remain as isolated packages as they are right now.

Mathematical view Vs. Physical View

Roozbeh Sanaei — Tue, 14 Aug 2007 03:06:28 -0400

Most of FEM Packages either Opensource or not which i have seen ever are based on phsycial aspect of finite element method. Interpreting Materials as their Stress- strain relation. i think in practice mathematical point of view in finite element iss more interesting. because its generality in defining elements depend on PDE which we want to solve it. and its clearity in defining ERROR and Refining the mesh. and its comparablity to other mathematical methods. I have not ever seen commerical finite element package which based on the MATHEMATICAL view. OF course COMSOL and FEMLAB could be such examples but their general PDE is very limited. DEAL.II and ALBERT of examples of opensource programs in this aspect. as their citation shows many users have used them by now and their bugs may be few. some examples of their usage which must of them are mechanical exists in their site and shows their applicablity in our way. its not bad to take a glance at them and use them in finite element projects. their expansion would result to more general finite element package we need in future.

COMSOL is available for fluid-structure interaction

Seungtae Choi — Thu, 02 Aug 2007 04:05:10 -0400

You can use COMSOL (http://www.comsol.com/) to simulate fluid-structure interaction. I have used COMSOL software to analyze a microfluidic pump operated by solid actuator. There is also another software, CFD-ACE. But, my colleagues prefer COMSOL. I hope this information is useful for you.

Seungtae

Open Source Software

Managers — Fri, 11 May 2007 08:01:32 -0400

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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.