Friday, February 28, 2014

IGA: people


  1. Thomas J.R. Hughes, ICES, University of Texas, Austin, USA Link
  2. Yuri Bazilevs, University of California, San Diego
  3. Alessandro Reali, Department of Civil Engineering and Architecture, University of Pavia, Italy
  4. Fehmi Cirak, Department of Engineering, Cambridge University, UK
  5. Angela Kunoth, Department of Mathematics, University of Cologne, Germany
  6. Ulrich Langer, Institute of Computational Mathematics, Johannes Kepler University Linz, Austria
  7. Jessica Zhang, Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, USA
  8. Bernd Simeon, Technische Universität Kaiserslautern, Germany
  9. Bernard Mourrain, INRIA Sophia Antipolis, France
  10. Hung Nguyen-Xuan, Computational Mechanics, University of Science Ho Chi Minh city, Vietnam
  11. Victor M. Calo, Associate Professor, AMCS & ErSE,  NumPor Center, KAUST
  12. David Benson, University of California, San Diego
  13. Tor Dokken, SINTEF ICT Department of Applied mathematics
  14. Trond Kvamsdal, Department of Mathematical Sciences, Norwegian University of Science and Technology

Wednesday, February 26, 2014

DYNA3D: 3D FEM large deformation

DYNA3D is an explicit, three- dimensional, finite element program for analyzing the large deformation dynamic response of inelastic solids and structures. DYNA3D contain 30 material models and 10 equations of state (EOS) to cover a wide range of material behavior. The material models implemented are: elastic, orthotropic elastic, kinematic/isotropic plasticity, thermoelastoplastic, soil and crushable foam, linear viscoelastic, Blatz-Ko rubber, high explosive burn, hydrodynamic without deviatoric stresses, elastoplastic hydrodynamic, temperature dependent elastoplastic, isotropic elastoplastic, isotropic elastoplastic with failure, soil and crushable foam with failure, Johnson/Cook plasticity model, pseudo TENSOR geological model, elastoplastic with fracture, power law isotropic plasticity, strain  rate dependent plasticity, rigid, thermal orthotropic, composite damage model, thermal orthotropic with 12 curves, piecewise linear isotropic plasticity, and inviscid two invariant geologic cap, orthotropic crushable model, Moonsy-Rivlin rubber, resultant plasticity, closed form update shell plasticity, and Frazer-Nash rubber model. The IBM 3090 version does not contain the last two models mentioned.

The hydrodynamic material models determine only the deviatoric stresses. Pressure is determined by one of ten equations of state including linear polynomial, JWL high explosive, Sack "Tuesday" high explosive, Gruneisen, ratio of polynomials, linear polynomial with energy deposition, ignition and growth of reaction in HE, tabulated  compaction, tabulated, and TENSOR pore collapse. DYNA3D generates three binary output databases. One contains information for complete states at infrequent intervals; 50 to 100 states is typical. The second contains information for a subset of nodes and elements at frequent intervals; 1,000 to 10,000 states is typical. The last contains interfaces data for contact surfaces.

Source: http://www.oecd-nea.org/tools/abstract/detail/nesc9909/

Tuesday, February 25, 2014

CFD / FEA Engineering, Consulting, Software Companies

A list of engineering, consulting and software in fields of CAD, FEA, CFD, FSI

USA 

Exa Corporationhttp://www.exa.com Atkins globalhttp://www.atkinsglobal.com/
Simutech grouphttp://www.simutechgroup.com/
JLR:  semiconductor, aerospace  http://www.jlrcom.com (Ansys)
STI Technologies Inc., mechanical engineering consulting firm,   http://www.sti-tech.com/
GLSV: FEA, CFD, Dynamics, Thermal, Acoustics http://www.glsv.com
SC Solutions: Structure, Systems and Control  http://www.scsolutions.com
Thermoanalytics: thermal   http://www.thermoanalytics.com
ATA Engineering: softs, services (large areas) http://www.ata-e.com
CFDmax  (CFD) www.cfdmax.com
CAE Associates https://caeai.com
Advanced Computational Solutions (ACS) Consulting, http://www.cfd-consulting.org
Price HVAC, http://www.price-hvac.com/
Aerodynamic solutions http://www.aerodynamic-solutions.com/
Innovative-cfd  http://www.innovative-cfd.com/
Navitek LTD, NavatekLtd.com
Bechtel, CFD, http://bechtel.com/
Combustion Science & Engineering, Inc., www.csefire.com
Acusim softwares, http://www.acusim.com/
Mader Consulting Co., http://www.mccohi.com
Flonomix Inc.,  http://www.flonomix.com/
LES additional module and simulation package, http://www.cascadetechnologies.com/
AECOM, http://www.aecom.com/
DEFORM: www.deform.com

CANADA

CFD Canada: CFD,   http://www.cfdconsulting.com/  (found by Kudriavtsev)
M & P Technologyhttp://cfd-world.ca
Maya Heat Transfer Technologies Ltd, http://www.mayahtt.com/

UK

Numerical Innovation Group, NING Research, www.ningresearch.co.uk ICON CFDhttp://www.iconcfd.com
BMT Fluid Mechanics Ltd www.bmtfm.com   (Malaysia office)
Geodigm http://www.geodigm.co.uk/
3D model, CAD, Surface http://www.3dmodelzone.com
Total Simulation , http://www.totalsimulation.co.uk/
Reaction Engines Ltd,
Zenotech, www.zenotech.com

BELGIUM
Optimization, http://www.n-side.com/
Aerospace, SABCA, http://www.sabca.be/

IRELAND
Numa Engineering Services, CFD, http://www.numa.ie,

FRANCE
CFD & Co, http://www.cfdandco.com/
Mecaflux, http://www.mecaflux.com/
RS2N, rs2n.com

GERMANY

Simtech grouphttp://www.simutechgroup.com/
CFD Software GmbH, Berlin Germany and Technische Universität Berlin, Germany
CDH AG http://www.cdh-ag.com/
Wave Engineering GmbH http://www.wave-engineering.de/
Volke Consulting Engineer GmbH http://www.volke-muc.de/
FluiDyna GmbH (Fluid consulting, hardware, HPC) http://www.fluidyna.com
SimScale GmbH, http://www.simscale.com
IANUS Simulation http://www.ianus-simulation.de/
engits, engineering and IT services, http://engits.eu/
LOHMEYER Consulting Engineers, http://www.lohmeyer.de/
ZF motion and mobility, http://www.zf.com/
Tian Building Engineering, http://www.building-engineering.de

NETHERLANDS
Code Product Solutionshttp://www.code-ps.com
Rubber Design, vibration and noise control, www.rubberdesign.nl
Pon Equipment and Pon Power, www.pon-cat.com
Oossanen Naval Architects b.v., http://www.oossanen.nl/

SPAIN


Compass Ingeniería y Sistemas, SA, Barcelona, Engineering Design consulting, http://www.compassis.com/

NORWAY
EDR Medeso, http://www.edr.no
Computational Industry Technologies (ComputIT) AS, Pirsenteret, Trondheim, Norway, www.computit.no

DENMARK
DHI, CFD http://www.dhigroup.com

SWEDEN
Minesto, http://www.minesto.se

SWITZERLAND

CADFEM, www.cadfem.ch
Ollon, CH-1867, Switzerland, http://www.caelinux.com


AUSTRALIA

Leap (Ansys CFD, PTC) http://www.leapaust.com.au/
Don Computing (Flow3D distributor) http://www.doncomputing.com/

NEW ZEALAND

Matrix  (Star-CD/CCM+) www.matrix.co.nz

INDIA

Hi-Tech CFD, http://www.hitechcfd.com/ CSM Technologies, http://www.csmpl.com/
Techzilon Training Solution, http://www.techzilon.com/ Mechartes Researchers Pvt. Ltd http://www.mechartes.com/
Zeus Numerix : CFD, FEA www.zeusnumerix.com

Learncax: ANSYS, FLUENT  http://www.learncax.com
DailyCadCamwww.dailycadcam.com
Lennox India Technology Centrewww.lennoxinternational.com
ASH-CFD solutions, 
Tripura consultancy and training services

SINGAPORE

Keppelwww.keppelom.com
ZEB Technology (S) Pte Ltd , http://zeb-tech.com/
CAD-IT Consultants (Asia) Pte Ltdwww.cadit.com.sg (ANSYS distributor)
SeaCAD Technologies Pte Ltd, http://www.seacadtech.com/
I-Mathhttp://www.imath-asia.com/    (COMSOL distributor)
Novatte, Visual Computing and HPChttp://www.novatte.com/
NING Research, http://www.ningresearch.sg/
Surbana, consulting (HVAC), http://www.surbana.com/
Lloyd's Register Global Technology Centre Pte Ltd, http://www.lr.org/about_us/research/singapore_gtc/
Evoqua Water Technologies Pte Ltd, CFD
Hatch Mott MacDonald, Prinicipal Mechanical Engineer , CFD
Agilent’s Life Sciences Group (LSG) , Mechanical Design Engineer (R&D) CFD
G-Energy Global Pte Ltd, HVAC
Leica geosystems , http://www.leica-geosystems.com/
Microfluidics, www.simtech.a-star.edu.sg
Seatech solutions, http://seatechsolutions.com
IGNESIS consultantshttp://ignisa.com/ (Fire, Building simulation)
Jimmy Lea, http://www.jimmylea.com/ (CFD, Singapore, Australia)

KOREA
MANN+HUMMEL Korea, www.mann-hummel.com

Imaginit http://www.imaginit.com/services/consulting-services/cfd-analysis-consulting


OTHERS

QATAR, CFD, http://www.flowpak.net/

List of Top Apple apps for Scientist and Researchers

Top apps (Apple iphone, ipad, Android) for Scientist and Researchers

  • Wunderlist (free): to-do list
  • Wolfram Alpha: computational knowledge engine
  • Server Auditor - ssh client and terminal
  • Logmein: remote access
  • TeX Writer (paid): LaTeX Editor and Compiler
  • Scanner Pro: scan
  • Notability: scribble annotations all over documents
  • Mindnode (free, limited): mind maps
  • Goodreader: add notes to PDFs
  • Evernote: log and capture anything
  • Easybib: bibliography, Citation generation
  • Dropbox: cloud, drive, sync
  • iWiki: Wikipedia apps in Apple 
  • Ruler: Measure dimension with mobile 
  • C++ : C++ Programming Language
  • WiBit.Net: C++ Programming
  • Visual Basic: Visual Basic Programming Language
  • R: R Programming Language

Monday, February 24, 2014

Nek5000, Free CFD solver

Nek5000 is an open-source (released under GPL) computational fluid dynamics solver based on the spectral element method and is actively developed at the Mathematics and Computer Science Division of Argonne National Laboratory. The code is written in Fortran77/C and employs the MPI standard for parallelism.

Features

  • scales to over a million processes
  • high-order spatial discretization using spectral elements
  • high-order semi-implicit timestepping
  • incompressible + low Mach number (variable density) flows
  • efficient preconditioners (multigrid + scalable coarse grid solves)
  • highly optimized computational kernels (e.g. matrix-matrix multiply)
  • low memory footprint and scalable memory design
  • high performance parallel I/O
  • ALE / moving meshes and free surface flow
  • accurate Lagrangian particle tracking
  • conjugate fluid-solid heat transfer
  • scalable communication kernels
  • build-in profiling analysis
  • interface to VisIt for parallel data analysis and visualization
  • interace to MOAB for advanced meshing capabilities

Source: nek5000.mcs.anl.gov 

Sunday, February 23, 2014

CFD/ FSI/ Fluid Dynamics/ Mechanics: Terms/ Concepts / Methods


Flow problems
  • Rayleigh Flow
  • Poiseuille flow
  • Stagnation Point Flow
  • the Stokes problem (diffusion equation)
  • Stokes flow (creeping flow)
  • Couette flow
  • Taylor-Couette flow
  • cavity flow
  • turbulent flow
  • Boussinesq
  • Steady vs unsteady flows
  • Compressible and incompressible flows
  • porous media flows
  • Rarefied flow vs transitional flow
  • Newtonian & Non-Newtonian flows
  • Multi-phase flows
  • Particle-Laden Flow
  • Flow with heat transfer
  • Boundary layer and transition
  • Hypersonic vs reacting flows
  • Combustion
  • Buoyant flows
  • coflow
  • Reactive flow
  • High-speed and chemical reacting flows
  • Environmental flows
  • Coastal and ocean fluid dynamics
  • Microfluidics
  • Hemodynamics (AmE), hæmodynamics (BrE)  - (blood flow)
  • Fluid-Solid Coupling
  • Fluid-Structure Interaction
  • Bingham fluid
  • Power-law fluid
  • D'Allembert's Paradox
Methods / Theories
  • Finite difference method (FDM)
  • Finite Element Method (FEM)
  • Finite Volume Method (FVM)
  • The arbitrary Lagrangian Eulerian (ALE) method
  • Spectral Element Method
  • Boundary element Method (BEM)
  • Vorticity based methods
  • Lattice gas/lattice Boltzmann (LB)
  • Spectral/hp Element 
  • Discontinuous Galerkin methods
  • High-resolution discretization schemes
  • High-order method
  • Meshfree methods
  • Smoothed-particle hydrodynamics
  • Stochastic Eulerian Lagrangian method
  • Blade element theory
  • Implicit iterative methods
  • Variational Multiscale Method (VMS)
  • hybrid Eulerian/Lagrangian Material Point Method
  • classical laminated plate theory (CLPT)
Boundary conditions
  • kinematic boundary condition
  • Dirichlet 
  • Neumann
  • wall 
  • inlet
  • outlet 
  • Axisymmetric
  • Symmetric
  • constant pressure
  • Pressure far-field 
  • Periodic/cyclic
  • Thermo baffle
  • Thermal
  • Radiation
  • discrete phase
  • Chemical reaction
  • zero flux 
Boundary conditions
  • viscous force
  • centrifugal force
  • coriolis force
Instability
  • Kelvin-Helmholtz instability
  • Rayleigh–Taylor instability
  • Taylor-Couette instability
Turbulence
  • Integral length scales
  • Kolmogorov scale (smallest dissipative scales)
  • Taylor microscales
  • Reynolds-averaged Navier-Stokes (RANS) 
  • Direct numerical simulation (DNS)
  • Large eddy simulation (LES)
  • Smagorinsky Model
  • sub-grid scale
  • Detached eddy simulations (DES) 
  • Reynolds stress model (RSM)
  • Probability density function (PDF) methods
  • k-epsilon
  • k-omega
  • Spalart-Allmaras
  • Boundary layer 
Multiphase/ Interface 
  • Level Set (LS) (Interface Capturing)
  • Volume Of Fluid (VoF) (Interface Capturing)
  • Moment Of Fluid (Interface Capturing)
  • Arbitrary Lagrangian Eulerian moving mesh approach (Interface Tracking)
  • Front Tracking (Interface Tracking)
  • Meshless particle methods (Interface Tracking)
  • Immersed boundary method 
Heat and Mass Transfer
  • Advection
  • Convection
  • Diffusion
Math
  • conservation, accuracy, fidelity, boundedness, stability, convergence
  • existence (solution exist)
  • singularity (smoothness)
  • Newmark-beta method
  • the Generalized Minimal Residual (GMRES) method.
  • Helmholtz decomposition
  • Least-squares
  • Galerkin
  • Leap-frog method (second order, explicit)
  • Crank-Nicolson method (second order, implicit)
  • Lax-Wendroff method (second order, explicit)
  • Third-order explicit Taylor-Galerkin method
  • Fourth-order implicit Taylor-Galerkin method
  • Burgers' equation

Saturday, February 22, 2014

Research Scientist Position / Postdoctoral Research Associate Position

Open Research Scientist Position

The University of Notre Dame, Center for Shock Wave-processing of Advanced Reactive
Materials (C-SWARM), is seeking a highly qualified candidate for a Research Scientist position
in the area of computational mechanics/physics and Verification/Validation (V&V) and
Uncertainty Quantification (UQ). C-SWARM is a newly established center of excellence by
National Nuclear Security Administration (NNSA) whose primary focus will be on the emerging
field of predictive science. The main mission of C-SWARM is to predict shock conditions under
which new materials can be synthesized using predictive computational models that are verified
and validated with quantified uncertainty on future high-performance Exascale computer
platforms.

The successful candidate will be key personnel in a team that is developing and
implementing adaptive, multiscale, high-performance (parallel) computational algorithms for
numerical solutions of chemo-thermo-mechanical PDE's with emphasis on complex
heterogeneous materials, such as heterogeneous reactive composites, etc. The candidate should
have proven supervisory skills with detailed knowledge of relevant technical area of science,
engineering, and computer technology, broad knowledge of computer hardware, system software,
and applications software for advanced scientific computing, proven management skills with the
ability to collaborate in a variety of relevant disciplines. Citizenship/visa restrictions apply.
Qualifications:

Ph.D. in Mechanical Engineering, Theoretical & Applied Mechanics, Applied Mathematics, Physics or related engineering/science discipline is required with a minimum of 3 years related work experience employing a variety of technical applications, publications in peer-reviewed journals and conference presentations.

Knowledgeable in computational nonlinear mechanics, numerical methods, fluid dynamics, and/or chemical kinetics and solid-solid phase transformations.

Knowledge of C/C++, Fortran and UNIX operating system is required.

Experience in parallel programming.


Open Postdoctoral Research Associate Position

Materials (C-SWARM), is seeking a highly qualified candidate for a Postdoctoral Research Associate position in the area of computational mechanics/physics and Verification/Validation (V&V) and Uncertainty Quantification (UQ). C-SWARM is a newly established center of excellence by National Nuclear Security Administration (NNSA) whose primary focus will be on the emerging field of predictive science. The main mission of C-SWARM is to predict shock conditions under which new materials can be synthesized using predictive computational models that are verified and validated with quantified uncertainty on future high-performance Exascale computer platforms.

The successful candidate will be key personnel in a team that is developing and implementing adaptive, multiscale, high-performance (parallel) computational algorithms for numerical solutions of chemo-thermo-mechanical PDE's with emphasis on complex heterogeneous materials, such as heterogeneous reactive composites, etc. The candidate should have detailed knowledge of relevant technical areas of science, engineering, system software, applications software for advanced scientific computing, broad knowledge of computer technology and hardware, and the ability to collaborate in a variety of relevant disciplines. Citizenship/visa restrictions apply.

Qualifications:

Ph.D. in Mechanical Engineering, Theoretical & Applied Mechanics, Applied Mathematics, Physics or related engineering/science discipline, publications in peerreviewed journals and conference presentations.

Knowledgeable in computational nonlinear mechanics, numerical methods, fluid dynamics, and/or chemical kinetics and solid-solid phase transformations.

Knowledge of C/C++, Fortran and UNIX operating system is required.

Experience in parallel programming.

Close Date:

Review of applications will begin immediately and continue until the position is filled.

Salary:

Salary will be commensurate with qualifications and experience.

Contact:

Interested applicants should send a CV with a cover letter, names of at least three references, and a summary of recent work. All applications should be submitted electronically (paperless process) as a single PDF document to:

Dr. Samuel Paolucci, C-SWARM Director
Tel: 574-631-8110
Email: paolucci@nd.edu

The University of Notre Dame is an Affirmative Action, Equal Opportunity Employer.
Women and minorities are encouraged to apply.



Friday, February 21, 2014

Paradyn: code high-performance

The Paradyn project develops technology that aids tool and application developers in their pursuit of high-performance, scalable, parallel and distributed software. The primary project, Paradyn, leverages a technique called dynamic instrumentation to efficiently obtain performance profiles of unmodified executables. This dynamic binary instrumentation technology is independently available to researchers via the Dyninst API.

Other research by the Paradyn project includes dynamic instrumentation of running operating system kernels, the Kerninst project, and the development of middleware for scalable, efficient, robust applications in the MRNet multicast/reduction network.

Source: http://www.paradyn.org/

Thursday, February 20, 2014

MayaVi Data Visualizer

The MayaVi Data Visualizer
http://mayavi.sourceforge.net/

Mayavi2: the next generation

MayaVi is not dead! Mayavi2 is the next generation of MayaVi. Mayavi2, is a full rewrite of the original MayaVi and provides far more scriptability, easier usage for common patterns, and easy embedding in Python applications.

Mayavi2 has been under very active development for a while now and has many more features than Mayavi-1.x. Please consult the Mayavi2 home page at http://code.enthought.com/projects/mayavi for more installation instructions and a user guide.

The following information and the information on this site pertains to the older MayaVi-1.x versions. Note that MayaVi-1.x is no longer under active development.

MayaVi1: the past

MayaVi1 is a free, easy to use scientific data visualizer. It is written in Python and uses the amazing Visualization Toolkit (VTK) for the graphics. It provides a GUI written using Tkinter. MayaVi is free and distributed under the conditions of the BSD license. It is also cross platform and should run on any platform where both Python and VTK are available (which is almost any *nix, Mac OSX or Windows).

Latest version: 1.5
Release date: 13 September, 2005
Read the announcement

Fairly stable CVS snapshots of MayaVi are obtainable from the download link on the left.

Features

An easy to use GUI.
Can be imported as a Python module from other Python programs and can also be scripted from the Python interpreter.
Provides modules to:
Visualize computational grids.
Visualize scalar, vector and tensor data.
Quite a few data filters are also provided.
Supports volume visualization of data via texture and ray cast mappers.
Support for any VTK dataset using the VTK data format. Works for rectilinear, structured, unstructured grid data and also for polygonal data. Both the original VTK data formats and the new XML formats are supported.
Support for PLOT3D data. Only the binary structured grid format works because of current limitations in VTK's vtkPLOT3DReader. Simple support for multi-block data is also incorporated.
Support for EnSight data. EnSight6 and EnSightGold formats are supported. Only single parts are supported at this time.
Multiple datasets can be used simultaneously. Multiple modules can be viewed simultaneously.
Support for data files belonging to a time series.
A pipeline browser with which you can browse and edit objects in the VTK pipeline. A segmented pipeline browser is used to make it easier to look at parts of the VTK pipeline.
Support for importing a simple VRML or 3D Studio scene. Texturing in VRML is not yet supported due to limitations in VTK's vtkVRMLImporter.
A modular design so you can add your own modules and filters.
A Lookup Table editor to customize your lookup tables easily while visualizing data!
An interactive data picker that lets you probe your data interactively.
A light manipulation kit that lets you modify the lighting of the visualization.
The visualization (or a part of it) can be saved and reused in the future.
Export the visualized scene to a Post Script file, PPM/BMP/TIFF/JPEG/PNG image, Open Inventor, Geomview OOGL, VRML files, Wavefront OBJ or RenderMan RIB files. It is also possible to save the scene to a vector graphic via GL2PS. This is only available if VTK is built with GL2PS support.
And a lot more! MayaVi can be easily modified to do things differently.
The name

MayaVi is pronounced as a single name as "Ma-ya-vee". It is not pronounced as "Maya" + "Vi". MayaVi has nothing to do with either Maya (the graphics/modelling tool) or Vi (the editor).

In Sanskrit "mayavi" means magician. The name wasn't exactly chosen for its meaning but was the result of a long and hard search with the author pestering a lot of people for suggestions. My sincere thanks to all of those who offered suggestions.

History

Earlier, the author had developed a similar visualization tool called VTK-CFD. This tool was originally intended for a Computational Fluid Dynamics (CFD) audience but had features that made it more of a generic data visualizer. After the VTK-CFD 0.6 version, it was completely redesigned, rewritten and renamed. The new design makes MayaVi a general scientific data visualizer.

Tuesday, February 18, 2014

Qt: Cross-platform application and UI development framework

Qt is a cross-platform application and UI framework for developers using C++ orQML, a CSS & JavaScript like language. Qt Creator is the supporting Qt IDE.
Qt, Qt Quick and the supporting tools are developed as an open source projectgoverned by an inclusive meritocratic model. Qt can be used under open source (LGPL v2.1) or commercial terms.

Monday, February 17, 2014

Doxygen: Generate documentation from source code

Generate documentation from source code

Doxygen is the de facto standard tool for generating documentation from annotated C++ sources, but it also supports other popular programming languages such as C, Objective-C, C#, PHP, Java, Python, IDL (Corba, Microsoft, and UNO/OpenOffice flavors), Fortran, VHDL, Tcl, and to some extent D.
Doxygen can help you in three ways:
  1. It can generate an on-line documentation browser (in HTML) and/or an off-line reference manual (in $\mbox{\LaTeX}$) from a set of documented source files. There is also support for generating output in RTF (MS-Word), PostScript, hyperlinked PDF, compressed HTML, and Unix man pages. The documentation is extracted directly from the sources, which makes it much easier to keep the documentation consistent with the source code.
  2. You can configure doxygen to extract the code structure from undocumented source files. This is very useful to quickly find your way in large source distributions. Doxygen can also visualize the relations between the various elements by means of include dependency graphs, inheritance diagrams, and collaboration diagrams, which are all generated automatically.
  3. You can also use doxygen for creating normal documentation (as I did for the doxygen user manual and web-site).
Doxygen is developed under Mac OS X and Linux, but is set-up to be highly portable. As a result, it runs on most other Unix flavors as well. Furthermore, executables for Windows are available.

Sunday, February 16, 2014

Octa: integrated simulation system for soft materials

Open, flexible and expandable system
  -Open source & Multi platform
Four meso-scale simulation programs
  -COGNAC   (Slide show of COGNAC)
  -PASTA   (Slide show of PASTA)
  -SUSHI   (Slide show of SUSHI)
  -MUFFIN   (Slide show of MUFFIN)
Additional simulation programs
  -NAPLES
  -KAPSEL
Common graphical user interface (Modeling platform)
  -GOURMET   (Slide show of GOURMET)
Zooming
  -Collaboration of many simulation programs

  (Slide show of zooming prototype, AMUSE)
APPLICATIONS
Stiffness of polymeric materials
Spin coating
Soft actuators
Micro-reactor chips
Morphology of tapered polymers
Morphology of 3-component systems
Reaction-induced phase separation
Deformation of crystalline lamellae
Morphology near a surface
Morphology of tri-block copolymers
Rheology of linear and star polymers
Cross linked polymers
Confined systems
Topological gels
Clay-polymer composites
Liquid crystals
.... etc.

 OCTA is an integrated simulation system for soft materials developed by the joint project of industry and academia funded by Ministry of Economy, Trade and Industry(METI), Japan. The objective of the project is to bridge microstructural (or molecular) characteristics of soft materials with their material characteristics by simulation and modeling. This objective was quite challenging.
 Soft materials are made of complex molecules consisting of millions of atoms, having internal structures at many levels, and exhibiting complex responses over time scales ranging from nano-seconds to years. Theoretical models for soft materials are quite diverse: atomistic models, coarse-grained models, continuum models, and other hybrid models have been proposed to deal with mesoscopic phenomena of soft materials. They are based on different physical concepts and have disparate data structures. Our task was to construct a simulation system by integrating such diverse models. This is the so called multi-scale, multi-physics problem in computational science and engineering.
 In this project, we tried to solve this problem by relying on the power brought by the collaboration of human beings. Rather than producing a software package dedicated to do a limited number of physical problems, we focused our attention on constructing a system which can grow in the future.
 OCTA consists of four simulation engines(COGNAC, PASTA, SUSHI, MUFFIN) and a simulation platform (GOURMET). The simulation engines can carry out the simulations of molecular dynamics, reptation dynamics, interfacial dynamics, gel dynamics, two-fluid dynamics etc, and the simulation platform gives a common graphical user interface to all engines, providing an environment for various engines to work together.
 In Japanese, the word "OCTA" means growth for future. OCTA is by no means complete: to cover the whole area in soft materials, engines need to be enhanced and the platform needs to be brushed up. We paid special attention to make the system customizable and expandable, so that the system can grow on its own. We very much hope that the system is useful for your research, and welcome any comments you have regarding the system.


Masao Doi
Project Leader, Nagoya University


http://octa.jp/

Saturday, February 15, 2014

Fluidity: an open-source, multiphase flow modelling


Fluidity is an open source, general purpose, multi-phase computational fluid dynamics code capable of numerically solving the Navier-Stokes equation and accompanying field equations on arbitrary unstructured finite element meshes in one, two and three dimensions. It is used in a number of different scientific areas including geophysical fluid dynamics, computational fluid dynamics, ocean modelling and mantle convection. It uses a finite element/control volume method which allows arbitrary movement of the mesh with time dependent problems, allowing mesh resolution to increase or decrease locally according to the current simulated state. It has a wide range of element choices including mixed formulations. Fluidity is parallelised using MPI and is capable of scaling to many thousands of processors on the UK national HPC service, HECToR. Other innovative and novel features are a user-friendly GUI and a python interface which can be used to calculate diagnostic fields, set prescribed fields or set user-defined boundary conditions.

Fluidity is a community-supported project focusing on the Ubuntu platform for central support, though some support on a best-effort basis can be given to users on other platforms. For full details of our support provision, see the systems support page.

Source: http://www3.imperial.ac.uk/earthscienceandengineering/research/amcg/software
Imperial College London

Friday, February 14, 2014

Fluid Mechanics: Lectures, Notes

Free lecture note, handout in CFD, Fluid Mechanics
Ocean, Maritime






Thursday, February 13, 2014

CAE, FEA, CFD: Nomenclature, Abbreviation

What is it stand for

ALE            Arbitrary Lagrangian-Eulerian
AMR           Adaptive Mesh Refinement
BEM           Boundary element method
CAD           Computer-aided design
CAE           Computer-aided  Engineering
CFD           Computational Fluid Dynamics
CFM          Computational Fluid Mechanics
CMC          Conditional Moment Closure
CSM          Computational Structure Mechanics
CMHD        Computational magnetohydrodynamics
DES            Detached eddy simulations
DEM           Discrete Element Method
DNS           Direct numerical simulation
DSMC        Direct Simulation Monte Carlo
DWR          Dual Weighted Residual
ELSA          Eulerian-Lagrangian Spray Atomization
FDM           Finite difference method
FEA            Finite Element Analysis
FEM           Finite Element Method
FFT            Fast Fourier Transformation
FLIP           Fluid-Implicit-Particle
FMM          Fast Multipole Method
FVM          Finite Volume Method
FVPM        Finite Volume Particle Method
FSI             Fluid Structure Interaction
GMRES      Generalized Minimal Residual (GMRES) method
IGA            Isogeometric Analysis
GFM           Ghost Fluid Method
HPC            High-performance Computing
LBM           Lattice Boltzmann methods
LES             Large eddy simulation
LPS             Local Projection Stabilization
MAC          Marker-and-cell method
MC             Monte Carlo
MD             Molecular Dynamics
MM            Molecular Mechanics
MMC         Metropolis Monte Carlo
MPM          Material Point Method
N-S            Navier-Stokes
NURBS      Non-Uniform Rational B-Splines
ODE           Ordinary Differential Equation
PDF            Probability density function
PDF            Pressure driven flow
PIC             Particle-in-cell
PISO           Pressure Implicit with Splitting of Operator

PRESTO     Pressure Staggering Option
PTC            Passive Turbulence Control 
RANS         Reynolds-averaged Navier–Stokes equations
REV            Reference Element of Volume
RMS           Root Mean Square
RSM           Reynolds stress model
RT              Rayleigh–Taylor (instability)
SAS            Scale-Adaptive Simulation
SDS            Stochastic Differential Systems
SEM           Spectral element method
SIMPLE     Semi-Implicit Method for Pressure Linked Equations
SGS            Sub-Grid Scales
SPH            Smoothed-particle hydrodynamics
TKE            Turbulence kinetic energy
TLBM         Thermal Lattice Boltzmann methods
TBL            Turbulent Boundary Layer
URANS      Unsteady Reynolds-averaged Navier–Stokes equations
VC              Vorticity Confinement
VIV             Vortex-induced vibration
VMS           Variational Multiscale Method
VOF            Volume of Fluid

EXPERIMENT
LIF               Laser-Induced Fluoresence
PIV              Particle Imaging Velocimetry
SMD            Sauter-mean Diameter (of product droplet)
LEDs            Light-emitting diodes

DIMENSIONLESS NUMBER
CFL             Courant-Friedrichs-Lewy
Fr                 Froude number
Re                Reynolds number
M                 Mach number
Nu                Nusselt number
Pe                Peclet number
Pr                 Prandtl number
St                 Strouhal number

MATH
ROSM         Reduced-Order Surrogate Model
FDKL          Frequency-Domain Karhunen-Loeve
POD            Proper Orthogonal Decomposition
SCI              Single-Composite Input



Wednesday, February 12, 2014

GeoPDEs: free IGA Isogeometric Analysis Package

GeoPDEs software

GeoPDEs is a suite of software tools for research on Isogeometric Analysis of PDEs. It provides a common and flexible framework for implementing and testing new isogeometric methods in different application areas. GeoPDEs is written in Octave and fully compatible with Matlab.
The suite consists of a set of interrelated packages. The main package, geopdes_base, defines the basic data-structures and methods, and should also serve as an entry point for understanding the implementation of an Isogeometric Analysis code.
Other packages deal with applications in linear elasticityfluid mechanics andelectromagnetism. A package specifically meant to allow handling multipatch NURBS geometries is also available.
Download and installation
To download the packages, and to get installation instructions, please go to thedownload page.
New releases of GeoPDEs may appear from time to time, either for adding new features to the original code, or for fixing bugs. If you want to receive information about new releases, please subscribe to the mailing list of GeoPDEs users.
The most recent version of GeoPDEs includes many changes to improve the efficiency, and also some important bug-fixes. We strongly recommend you to keep your software updated. A list of all the changes up to date can be found in the release notes.
Help
The code has been released along with an article [dFRV11] explaining its architecture, its design and its main features, and providing various usage examples. We have also prepared a new preprint version that explains the changes included in GeoPDEs 2.0.0, and how the examples were upgraded to this version. It is always possible to download the journal version of the paper, but this one will not be updated.
Although it is not a complete documentation, the paper can be read as a brief user's guide. The preprint version also contains some useful tables that summarize the most important information. More detailed help can be found in the documentation page.
Development
GeoPDEs is now being mainly developed and maintained by Rafael zquez (IMATI-CNR).The conception of the software, its development and maintenance has been funded by the European Research Council through the FP7 Ideas Starting Grant: GeoPDEs - Innovative compatible discretization techniques for Partial Differential Equations, under the coordination of Annalisa Buffa (IMATI-CNR).
Very important contributions have been made by Carlo de Falco and Alessandro Reali. The following people have also contributed to the development of GeoPDEs, either by writing lines of code, testing the packages, or giving some advice: Andrea Bressan, Annalisa Buffa, Durkbin Cho, Timo Lähivaara, Massimiliano Martinelli, Marco Pingaro, Giancarlo Sangalli.
Some of our contributors have received additional support from the two following grants:FP7 Ideas Starting Grant: ISOBIO - Isogeometric Methods for Biomechanics, coordinated by Alessandro Reali, and FIRB Futuro in Ricerca (MIUR Grant) RBFR08CZ0S - Discretizzazioni  Isogeometriche per la  Meccanica del Continuo, coordinated by Giancarlo Sangalli.
License
GeoPDEs is free (as in "free speech") software released under the terms of the GNU GPL license (v3).
How to contribute
GeoPDEs has been developed as a part of our research, and it is funded by our respective institutions. The best way to support us is by citing our work [dFRV11] in any paper where GeoPDEs is used to obtain results.
We also encourage contributions that can help to improve the code or the documentation, and to make GeoPDEs more useful. See the contributions page for details.

Tuesday, February 11, 2014

PETSc: The Portable, Extensible Toolkit for Scientific Computation

PETSc: The Portable, Extensible Toolkit for Scientific Computation,  Argonne National Laboratory
Source: http://www.mcs.anl.gov/petsc/


PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. It supports MPI, shared memory pthreads, and NVIDIA GPUs, as well as hybrid MPI-shared memory pthreads or MPI-GPU parallelism.
- Scientific applications that use PETSc
  • TAO - Toolkit for Advanced Optimization
  • SLEPc - Scalable Library for Eigenvalue Problems
  • fluidity - a finite element/volume fluids code
  • OpenFVM - finite volume based CFD solver
  • OOFEM - object oriented finite element library
  • libMesh - adaptive finite element library
  • MOOSE - Multiphysics Object-Oriented Simulation Environment developed at INL built on top of libmesh on top of PETSc
  • FEniCS - sophisticated Python based finite element simulation package
  • DEAL.II - sophisticated C++ based finite element simulation package
  • PHAML - The Parallel Hierarchical Adaptive MultiLevel Project
  • Chaste - Cancer, Heart and Soft Tissue Environment
  • PyClaw - A massively parallel, high order accurate, hyperbolic PDE solver
  • PetIGA - A framework for high performance Isogeometric Analysis
  • petsc4py from Lisandro Dalcin at CIMEC
  • Elefant from the SML group at NICTA
  • jpetsctao from Hannes Sommer
  • Packages that PETSc can optionally use



- Features of the PETSc libraries (and a recent podcast)
- Linear system solvers accessible from PETSc
- Related packages that use PETSc


Python Bindings


Java Bindings


Monday, February 10, 2014

Microfluidics / Nanofluidics: CFD, Useful information

Center / laboratory

Lecture / Handout


People:

  • Prof. Roland Zengerle, University of Freiburg, Department of Microsystems Engineering – IMTEK, Laboratory for MEMS Applications, editor of the journal “Microfluidics and Nanofluidics”,  www.imtek.de/laboratories/mems-applications/staff/personal-websites/zengerle?set_language=en
  • Prof Nam-Trung Nguyen,  Queensland Micro- and Nanotechnology Centre, Griffith, https://dl.dropboxusercontent.com/u/9992589/index.htmhttp://www.griffith.edu.au/science-aviation/queensland-micro-nanotechnology-centre/staff/prof-nam-trung-nguyen
  • Yoshinobu Baba, Nagoya University
  • George Whitesides, Harvard University
  • Joanna Aizenberg, Harvard University
  • Dave Weitz, Harvard University
  • Howard Stone, Princeton University
  • Jose Bico, ESPCI
  • Cees Dekker, Delft University
  • Nam-Trung Nguyen, Professor and Director, Queensland Micro and Nanotechnology Centre
  • Elisabeth Charlaix, L'Université Joseph Fourier de Grenoble
  • Wilhelm Huck, University of Nijmegen
  • Demetri Psaltis, EPFL
  • Oliver Schmidt, University of Dresden
  • Ping Sheng, HKUST
  • Matthias Wessling, University of Aachen
  • Prof. Detlef Lohsehttp://pof.tnw.utwente.nl
  • Prof. Albert van den Berghttp://www.utwente.nl/ewi/bios/
  • Prof. Einar Kruis, Institute of technology for Nanostructures, Universität Duisburg-Essen, link
  • Helene Andersson Svahn, KTH Royal Institute of Technology, Sweden
  • Bruno Andreotti, ESPCI
  • Robert H. Austin, Princeton University
  • Charles Baroud, École Polytechnique Petra Dittrich, ETH Zurich
  • Luca Biferale, University of Tor Vergata
  • Lydéric Bocquet, University of Lyon
  • Henrik Bruus, Technical University of Denmark
  • Vince Craig, Australian National University
  • Anton Darhuber, Eindhoven University of Technology
  • Petra Dittrich, ETH Zurich
  • Albert Folch, University of Washington
  • James Friend, RMIT
  • José Manuel Gordillo, Universidad de Sevilla
  • Steffen Hardt, Technische Universität Darmstadt
  • Jongyoon Han, MIT
  • Stephan Herminghaus, Max Planck Institute for Dynamics and Self-Organization
  • Ian Hutchings, University of Cambridge
  • Karin Jacobs, Saarland University
  • Oliver Jensen, University of Manchester
  • Takehiko Kitamori, University of Tokyo
  • Madhavi Krishnan, ETH Zurich
  • Thomas Laurell, Lund University
  • Gary Leal, University of California, Santa Barbara
  • Abraham P. Lee, University of California, Irvine
  • Dominique Legendre, Institut de Mécanique des Fluides de Toulouse
  • Andreas Manz, KIST Europe
  • Andrew deMello, ETH Zurich
  • Harp Minhas, Lab on a Chip
  • Sumita Pennathur, University of California, Santa Barbara
  • Steve Quake, Stanford University
  • David Quéré, ESPCI
  • Philippe Renaud, École Polytechnique Fédérale de Lausanne
  • Hans Riegler, Max Planck Institute of Colloids and Interfaces
  • Juan Santiago, Stanford University
  • Shuichi Shoji, Waseda University
  • Todd Squires, University of California, Santa Barbara
  • Federico Toschi, Eindhoven University of Technology
  • Olga Vinogradova, Moscow State University
  • Jerry Westerweel, Delft University of Technology
  • Paul Yager, University of Washington
  • Sandip Ghosal, Associate Professor of Mechanical Engineering and (by courtesy) Engineering Sciences and Applied Mathematics, http://ghosal.mech.northwestern.edu/
  • Juan G. Santiago, Mechanical Engineering Department, Stanford University, http://microfluidics.stanford.edu/People/People.html
  • Prof. Yong Kweon Suh, Department of Mechanical Engineering, Office: RS216 at Dong-A Univ., Tel    : (051) 200-7648, E-mail : yksuh@dau.ac.kr, Homepage : http://cfdlab.donga.ac.kr
  • Duong A. Hoang: (OpenFOAM) http://cheme.nl/ppe/people/duong.shtml
  • David A. Weitz, Mallinckrodt Professor of Physics and of Applied Physics, https://www.physics.harvard.edu/people/facpages/weitz
  • Jayne Wu, Associate Professor, Dept. of Electrical and Computer Engineering, Univ. of Tennessee, Knoxville, http://web.eecs.utk.edu/~jaynewu
  • Dr Jong-Leng Liow, Senior Lecturer, School of Engineering and Information Technology, UNSW Canberra, https://research.unsw.edu.au/people/dr-jong-leng-liow
  • Dr. Liu Cheng-Hsien, Professor National Tsing Hua University (Taiwan), Lab Chip for biomedical applications 

  • Nancy Allbritton, UNC Chapel Hill, USA
  • Robert Austin, Princeton University, USA
  • Chia Chang, University of Notre Dame, USA
  • Chi-Ming Ho, UCLA, USA
  • Takehiko Kitamori, University of Tokyo, Japan
  • Andrew de Mello, ETH Zürich, Switzerland
  • Hywel Morgan, University of Southampton, UK
  • Jian-Hua Qin, CAS, Dalian, China
  • Ying-Chih Chang, GRC, Academia Sinica, Taiwan
  • Ling Chao, NTU, Taiwan
  • Ji-Yen Cheng, RCAS, Academia Sinica, Taiwan
  • Patrick Doyle, MIT, USA
  • Shih-Kang Fan, NTU, Taiwan
  • Haiping Fang, CAS, Shanghai, China
  • Chih-Chen Hsieh , NTU, Taiwan
  • I-Ming Hsing, HKUST, Hong Kong
  • Chih-Yung Huang, NTHU, Taiwan
  • Noo Li Jeon, Seoul National University, Korea
  • Hong-Ren Jiang, NTU, Taiwan
  • Xinyu Jiang, NCNST, China
  • Noritada Kaji, Nagoya University, Japan
  • Gwo-Bin Lee, NTHU, Taiwan
  • Chwee Teck Lim, National University of Singapore
  • Keng-Hui Lin, IoP, Academia Sinica, Taiwan
  • Hidehiro Oana, University of Tokyo, Japan
  • Jonas Tegenfeldt, Lund University, Sweden
  • Fan-Gang Tseng , NTHU, Taiwan
  • Hsiang-Yu Wang, NCKU, Taiwan
  • Chung-Yi Wu, GRC, Academia Sinica, Taiwan
  • Daniel Ou-Yang, Lehigh University, USA
  • Yao-Joe Yang, NTU, Taiwan
  • Zilin Chen, Wuhan University, China
  • Larry Cheng, Oregon State University, USA
  • Zachary Gagnon , Johns Hopkins University, USA
  • Dmitry Kopelevich, University of Florida, USA
  • James Lee, Ohio State University, USA
  • Leslie Yeo, RMIT, Australia
  • Gilad Yossifon, Technion University, Israel

  • Panagiota Angeli University College London UK 
  • Lucien Baldas           INSA Toulouse France
  • Gian Piero Celata ENEA Italy
  • Tara Dalton           University of Limerick Ireland
  • Arjan Frijns Technical University Eindhoven Netherlands 
  • Ronan Grimes University of Limerick Ireland
  • Anne-Marie Gué LAAS CNRS France
  • Ibrahim Hassan Concordia University USA
  • Weiling Luan East China University of Science and Technology China
  • Denis Maillet Institut National Polytechnique de Lorraine France
  • Marco Marengo University of Bergamo Italy
  • Pierre Perrier University Aix-Provence France 
  • Jeff Punch University of Limerick Ireland
  • Massimilano Rossi University of the Bundeswehr Germany
  • Christof Serra University of Strasbourg France
  • Zhan-hua Silber-Li Chinese Academy of Sciences China
  • Jason Stafford Bell Laboratories Alcatel Lucent Ireland
  • Sedat Tardu University of Grenoble France
  • Dimitris Valougeorgis University of Thessaly Greece
  • Patrick Walsh University of Limerick Ireland
  • Paul Watts Nelson Mandela Metropolitan University South Africa
  • Robert Wootton ETH Zurich Switzerland
  • Leslie Yeo Monash University Australia
  • Yonghao Zhang University of Strathclyde UK
  • Nam-Trung Nguyen Griffith University Australia
  • Yoav Peles Rensselaer Polytechnic Institute USA
  • Wolfgang Hilber JKU Linz Austria
SINGAPORE

  • Cheng Kuo LEE, National University of Singapore
  • Chia-Hung CHEN, National University of Singapore
  • Jonathan HOBLEY, Institute of Material Research & Engineering
  • Evert KLASEBOER, Institute of High Performance Computing
  • Heow Pueh LEE, National University of Singapore
  • Kian Meng LIM, National University of Singapore
  • Ai-Qun LIU, Department of Electrical & Electronic Engineering, Nanyang Technological University
  • Claus-Dieter OHL, Nanyang Technological University
  • Siew-Wan OHL, Institute of High Performance Computing
  • Zhiping WANG, Singapore Institute of Manufacturing Technology
  • Eric Peng Huat YAP, DSO National Labs
  • Yuanjin ZHENG, Nanyang Technological University,  Singapore
COMPANIES
COURSES