#semphyssci
Andrew Walker (video http://vimeo.com/35562270 ) presented “FoX, CML, and semantic tools for atomistic simulation” at the Semantic Physical Science symposium. Andrew has taken on from Toby White as the “Doctor Who” of FoX, the FORTRAN library for managing XML input and output. FoX allows for domain-specific XML conventions and supports a subset of CML (scalar/array/matrix, module/list, and molecule). There are now about 12 codes which have substantial conversion to allow CML output.
In this presentation Andrew describes the philosophy and current status of FoX.
Here I’ll take time to thank Andrew for continuing the work on FoX. Without that I don’t think we could expect groups such as PNNL and Daresbury to commit to supporting CML. There is now a critical mass of users and new features are clearly worth the investment.
The Time-annotated talk (on VIMEO you can click times)
0:00 Intro and data management
1:00 traditional example, glue code
2:00 Code in FORTRAN, require XML. Only tool C compiler
3:00 options
3:30 FORTRAN-XML is most attractive choice
3:50 Homage to Toby White and Alberto Garcia
5:30 Benefit of XML
6:00 example of XML code
6:40 benefits of XML
7:00 CML convention for atomistic simulation
8:00 overview of FoX
8:50 Codes using FoX – about 12
10:00 SIESTA tests new version against CML
11:00 example of output transformations (uses XSLT)
11:50 SIESTA output
12:30 Jmol output
12:50 AMBER example
13:50 Where to get FoX and completely reusable (BSD licence) with mailing list.
14:36 end (and some questions)