Peter Murray-Rust
Cambridge, UK
wwmm.ch.cam.ac.uk
See Wikipedia entry: en.wikipedia.org/wiki/Peter_Murray-Rust - includes photo

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  • Video comment
    4 weeks ago
    Peter Murray-Rust commented on FoX CML and atomistic Simulation, Andrew Walker, Bristol UK

    TABLE OF CONTENTS (times are clickable)

    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 attrictive 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)

  • Video comment
    4 weeks ago
    Peter Murray-Rust commented on CML in computational materials science, Martin Dove

    TABLE OF CONTENTS (times are clickable)

    1:10 Scientific Example materials that shrink when heated
    1:40 plotted simulated volume against temperature
    2:30 no reason not to plot lots of points
    2:50 workflow
    3:20 can launch hundreds of jobs
    3:40 hard bit is extracting results
    4:00 traditional output file
    5:00 traditionally might have to read code to understand
    5:50 traditionally bad practice is tolerated
    5:45 CML makes extracting data easy
    6:00 Example of CML
    6:30 input parameters and metadata
    7:00 typical CML scalar property
    8:00 Codes whih produce CML
    8:15 introduces FoX; writng CML is simple
    9:45 otherwise have to write parsers
    10:10 Toby White's ccViz
    11:45 Final quantities (e.g. Diffusion Coefficient)
    12:00 Graphs
    12:45 can send marked up file for collaboration
    13:00 very good to avoid training students on legacy
    13:20 extraction data (xtract will create a CSV file)
    15:00 Martin was able to present this to high-school students - they could run hundreds of jobs
    15:50 Martin cares because it makes lives easier
    16:15 CML is "Best kept secret"
    16:40 end

  • upload
    4 weeks ago
    Peter Murray-Rust uploaded Untitled
  • Video comment
    1 month ago
    Peter Murray-Rust commented on Semantic Crystallography, Brian McMahon at Semantic Physical Science, 2012-01-12, Cambridge

    Fuller discussion in blog post:
    blogs.ch.cam.ac.uk/pmr/2012/01/23/brian-mcmahon-publishing-semantic-crystallography-every-science-data-publisher-should-watch-this-all-the-way-through/

  • Video comment
    1 month ago
    Peter Murray-Rust commented on Semantic Crystallography, Brian McMahon at Semantic Physical Science, 2012-01-12, Cambridge

    TABLE OF CONTENTS (Click time to go to place in video)

    0:00 Title
    0:40 International Union of Crystallography
    1:08 CIF
    3:36 CIF Syntax and dataTypes
    4:30 Publishing with CIF
    6:41 Demonstration: CheckCIF
    12:02 Interactive Chemical validation
    14:42 Linking data to journal article and search for novelty of data
    15:08 Jmol display applet
    21:03 Supplementary data
    21:47 PublCIF a tool to merge data and text and annotate them
    27:08 end

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