Quantum Espresso!

Quantum Espresso I just got email from Brandon Wood about an open source project called Quantum Espresso (formerly known as PWSCF), which is a rather extensive open-source project for DFT-based electronic structure calculations. It appears to be a refactoring of some established codes (PWscf, PHONON, CP90, FPMD, Wannier) that have been developed and tested by some of the original authors of novel electronic-structure algorithms – from Car-Parrinello molecular dynamics to density-functional perturbation theory – and applied in the last twenty years by some of the leading materials modeling groups worldwide.

There are definitely some scientific niches which desperately need open source codes (plane wave DFT is one of the ones that comes to mind), so I’m very pleased to learn about this project.

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Quantum-Espresso

Quantum ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft).
Find Quantum-Espresso at: http://www.quantum-espresso.org

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New Software: Reference Tools, Atomic Physics, and Engineering

Some new software to point out today:

  • In the Tools section, we have a new link to cb2bib a tool for rapidly extracting unformatted bibliographic references from email alerts, journal web pages, and PDF files.
  • In the Atomic & Molecular Physics section we have a new link to FELLA, which stands for Free Electron Laser Atomic, Molecular, and Optical Physics Program Package. FELLA is a joint project of Christian Buth from LSU and Robin Santra at Argonne National Laboratory.
  • In the Engineering section, we have two new links, one for View3D, a command-line tool for evaluating radiation view factors for scenes with complex 2D and 3D geometry, and one for OSIV a program that performs cross-correlation analysis of particle image velocimetry (PIV) images.

Check them out, and as always, be sure to suggest your favorite open source scientific software!

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cb2bib – From clipboard to BibTeX: A tool for extracting bibliographic references

From clipboard to BibTeX: A tool for rapidly extracting unformatted bibliographic references from email alerts, journal web pages, and PDF files. The cb2Bib facilitates the capture of single references from unformatted and non standard sources. Output references are written in BibTeX. Article files can be easily linked and renamed by dragging it onto the cb2Bib window. Additionally, it permits editing and browsing BibTeX files, searching references and the contents of linked files, and cite them into document editors.
Find cb2bib – From clipboard to BibTeX: A tool for extracting bibliographic references at: http://www.molspaces.com/cb2bib/index.html

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FELLA (Free Electron Laser Atomic, Molecular, and Optical Physics Program Package)

The software package FELLA has been written for basic research in atomic, molecular, and optical physics. The atomic physics programs treat the atomic electronic structure in Hartree-Fock-Slater approximation and the interaction of electrons with light of up to two colors. The molecular physics programs treat the x-ray absorption by laser-aligned molecules. An optical physics code describes the propagation of a laser and x-rays through a gaseous medium. Especially, FELLA has been inspired by the upcoming x-ray free electron lasers to study atoms and molecules in their light in combination with intense optical lasers. However FELLA is more general and has been used so far to study atoms and molecules in the light of third-generation synchrotrons.
Find FELLA (Free Electron Laser Atomic, Molecular, and Optical Physics Program Package) at: http://chemistry.anl.gov/Fundamental_Interactions/FELLA_main.shtml

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View3D: calculation of radiation view factors in 2D and 3D

View3D is a command-line tool for evaluating radiation view factors for scenes with complex 2D and 3D geometry. It uses an adaptive integration method to calculate the view factors between faces where there is partial obstruction from inbetween faces.

This program can be used to calculate the view factors (aka shape factors/configuration factors/form factors) for radiant heat transfer in diffuse grey enclosures.
Find View3D: calculation of radiation view factors in 2D and 3D at: http://view3d.sourceforge.net/

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Open Source Image Velocimetry

OSIV is a program written to perform cross-correlation analysis of particle image velocimetry (PIV) images. The program was designed to be both very modular and quite efficient. It incorporates most of the tried-and-true algorithms and some of the more recent additions to the PIV toolkit.
Find Open Source Image Velocimetry at: http://osiv.sourceforge.net

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Earmarks for Science

At the debate last night, John McCain brought up (twice!) for special scorn an example of spending on earmarks. His target? The “overhead projector for a planetarium”. It wasn’t the first time he’s brought up this earmark request up either. Bad Astronomy had a good post on how McCain’s comments on planetaria make him “literally antiscience”. The projector in question is hardly your run-of-the-mill overhead projector. The Adler planetarium in Chicago has a “Sky Theater” or a hemi-spherical dome on which it can project just about anything if you have the right equipment. Notre Dame (where I teach) has a very similar set-up in our digital visualization theater. The projectors we use were modeled on the current system at the Hayden planetarium, and just to give you some scope, we have a 50-foot high domed ceiling for a hexagon array of chairs that seats 136 students. The system is run with 10 computers, 8 of which do nothing but render 3D objects and transform them for hemispherical projections. It was a million dollar facility that goes a long way toward making all aspects of science visible to our students. In fact, as earmarks go, the planetarium projector at the Adler is a lot less offensive than some other projects (notably a certain bridge in Alaska).

In the past, McCain has also targeted for scorn an expenditure to study the “DNA of bears in Montana”. To be fair, other earmarks have also been his target: The Woodstock museum, and the bridge to nowhere (at least until he picked a running mate who was in favor of that same bridge) have also been the targets of McCain’s anti-pork ire. But last night, he seemed to express a special loathing for earmarks for science.

Now, a good case can be made (and should be made) that using earmarks to fund basic science research or science outreach is just bad policy. In fact, I’d be happier if the budgets for science-related earmarks were turned over to the NSF in order to fund peer-reviewed and merit-based proposals. But if the earmarks are the only way to fund science outreach projects like the Adler’s planetarium, then count me in. It is certainly a better use of money than David Vitter’s proposed earmark of $100,000 for a group that promotes “creation science”. In fact a list of examples of religious earmarks pointed out by Americans United for the Separation of Church and State are all worse than the Adler planetarium project.

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Exhibit: make your data web-accessible

Exhibit Logo David Karger‘s lab at MIT has developed some neat web software called exhibit, which is designed to let non-ultra-sophisticated individuals publish data in ways that make it immediately accessible and interactive for people encountering it on the web. With exhibit, a scientist with a lot of data doesn’t need to manage a database (mysql, etc.) and program a front end for it. Instead, they can put a data file (as simple as a spreadsheet) and a presentation file (written in basic html) on their web site and they’re done. There are a couple of great examples including an interactive elements table that one of Karger’s undergraduates put together.

Exhibit is a three-tier web application framework written in Javascript, which you can include like you would include Google Maps. The integration with Google maps is quite impressive. One can imagine using it to display geographic or other spatial data. In fact, here’s an exhibit of Danish monthly weather records since 1874. And here’s a great example of exhibit being used to display a bibliography for the MIT haystack group.

Other useful related projects are Timeplot and Timeline for placing interactive time data on a web page.

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OpenFVM

OpenFVM is a general open source three-dimensional CFD solver (for Linux and Windows). It uses the unstructured finite volume method to simulate non-isothermal transient flow. Gmsh is used for pre- and post- processing.
Find OpenFVM at: http://openfvm.sourceforge.net/

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