Condensed Matter Dynamics

Downloads

"A child of five would understand this.
Send someone to fetch a child of five."

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Thesis

Here is my Thesis, as was accepted by the University of York on the 13th April 2007 (Submitted December 2006).

  • When citing this, please also cite the two papers listed below.
    • A Genetic Algorithm for Crystal Structure Prediction. PDF File

Here is my Thesis template, designed for the University of York.

  • Thesis template (Linux compatible) Tar-Ball
  • Thesis template (windows compatible) Zip-File
 

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Papers

Here is a list of the papers that I have in various stages of preparation/publication.

  • N.L. Abraham and M.I.J. Probert, A Periodic Genetic Algorithm with Real-Space Representation for Crystal Structure and Polymorph Prediction, Phys. Rev. B   73, 224104 (2006)
    • The Physical Review B version of the paper can be downloaded from their website. This also contains a full bibliograhpy.
    • A preprint of this paper is availible to download from arXiv.org at cond-mat/0605066.
  • N.L. Abraham and M.I.J. Probert, Improved real-space genetic algorithm for crystal structure and polymorph prediction, Phys. Rev. B   77, 134117 (2008)

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Talks

Here are the talks that I have presented so far.

  • "Why PES-imism is a Good Thing." pdf
  • "Genetic Algorithms for Surfaces and Bulk." pdf
  • "Genetic Algorithms: Educational Fun for all the Family" pdf
  • "A Real-Space Genetic Algorithm for Crystal Structure Determination" pdf
    This is the talk that I gave at the 2006 APS March Meeting in Baltimore.
 

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Conference Posters

These are the posters that I have presented various conferences.

  • Global Optimisation of Molecular Clusters. pdf
  • A Genetic Algorithm for Surface Reconstructions and other Periodic Systems. pdf
  • A Real-Space Genetic Algorithm for Crystal Structure Determination. pdf
 

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Group Seminar Notes

These are the handouts that I have provided when giving group seminars.

  • Introduction to Genetic Algorithms. pdf
  • Polar Stratospheric Chemistry: Catalytic Reaction on Ice. pdf
  • Visualisation of the Potential Energy Surface. pdf
  • Real-Space GA's and expansion using Periodic Boundary Conditions. pdf
  • Genetic Algorithms for Surface Reconstruction. pdf
 

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Help Files for Programming in Fortran 90

Here are some help files I have written for the 1st Year Fortran 90 course.

  • How to set up Exceed 6.0 on Windows2000 campus machines.
    pdf file (recommended) or text file
    Please note: for this to work you must have already registered for tower, which you can do on the Registration page at the electronic infodesk
     
  • Using NEdit for Fortran90 programming.
    pdf file (recommended) or text file
     
  • Very simple guide for getting started with GNUPlot.
    pdf file (recommended) or text file
    A more detailed website on gnuplot can be found through the links section.
     
  • How to use Pine from Tower.
    pdf file (recommended) or text file
    Please note: for this to work you must have already registered for tower, which you can do on the Registration page at the electronic infodesk
 

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Shell Scripts

  • Prompt tips for bash and tcsh, and some stuff for Emacs and LATEX. pdf

Various C-Shell scripts and FORTRAN 90 programs that I have written that do useful stuff. These are all available in a tarball or download individually from from here

  • Submission script for ERIK to run parallel jobs:
    submit.csh or download here NOTE: The use of mpirun is no longer required, and mpiexec is now the correct useage. I haven't got around to changing these scripts though.
  • A script that converts the atom type in .xyz files to He:
    Ne2He.csh or download here
  • A script does a ps -U on all nodes of erik, and then reports back the results.
    ps.sh or download here
  • A script that generates a moving gnuplot file of radial distribution functions from some of my output files:
    gnuscript.csh or download here
  • A script that generates a gnuplot script of my energy output and then runs it to create an eps file via pstex:
    val2eps.csh or download here
    • This requires one awk script and the basic gnuplot script:
      gnu_gen.awk or download here
      blank.gnu or download here
    • It also requires these two scripts, which I didn't write but are very useful anyway:
      pstex2eps Creates an .eps file from a .pstex file (download here ).
      fixbb The .eps files from pstex2eps sometimes need the bounding box fixing (download here ).
  • A script that copies data files from a remote machine to the local machine.
    getfiles.csh or download here
  • A script that runs a program, and then re-nice's it to a user defined value.
    rc.csh or download here
  • A script that works out the memory useage of a process and plots it to a file. With thanks to Matt Probert.
    check_size or download here
  • A script that takes all the subdirectories within the current working directory, tar and gzips them while removing the files, and then removes the original empty directory, leaving only a .tgz file.
    tardir.csh or download here
  • A script that takes data from a file and reorders it, say the data is of type
    dataset 1   line 1
    dataset 2   line 1
    dataset 3   line 1
    dataset 1   line 2
    dataset 2   line 2
    dataset 3   line 2
    dataset 1   line 3
    dataset 2   line 3
    dataset 3   line 3
    then this script will rearrange so that there are (in this case) three files, each arranged like
    dataset 1   line 1
    dataset 1   line 2
    dataset 1   line 3
    beamsift or download here This script was requested by Chris to help him analise some data.
  • A script that converts .dvi files to .pdf files
    dvi2pdf or download here
  • A bash script that converts the CASTEP GA output to the CASTEP cell format. This is my first bash script.
    ga2cell.bash or download here

Here are some FORTRAN 90 programs I have written to do things that I find useful. I should probably learn Perl and re-write them in that. These are quite old, and contain a bit of bad programming practice, but they basically do the job.

  • A FORTRAN 90 program that generates XxYxZ supercells from primitive .xyz file and a .cell file.
    surfgen.f90 or download here
  • A FORTRAN 90 program that tessellates a structure in a .xyz file format to aid visualisation.
    tess.f90 or download here
 

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Miscellaneous

These are some random things that I've done.

  • Recipe for Cinnamon Balls. pdf
    A traditional recipe, which can be found in "The Complete International Jewish Cookbook" by Evelyn Rose, along with loads of other mouth watering recipes. Here is the amazon.co.uk listing.
  • Recipe for Meat-Balls. pdf
    Here is my recipe for meat-balls, as requested by James.
     
  • Lunchtime bonus question, caption competition and Friday challenge things I have had published on the BBC News magazine site. Collected here to hide my embarrassment. The BBC have discontinued the LBQ now, although the caption competition is still going.
  • All the quotes from the top of each page have been collected here along with references.
  • York has a mutant duck, which resides on campus. I took a snap of it with some other ducks.