This is the README file for the KhovanovSteenrod program.

Copyright (C) 2011,2012 Robert Lipshitz and Sucharit Sarkar.
Contact: lipshitz@math.columbia.edu, sucharit@math.columbia.edu

Copying and distribution of this file, with or without modification,
are permitted in any medium without royalty provided the copyright
notice and this notice are preserved.


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Here is a step by step guideline on how to recompute the data. Note,
this process will regenerate the files alldata.sage, allhom.sage and
result.sage.

-Install Sage. (Visit http://www.sagemath.org/)

-Install the Sage package CHomP. (Visit
http://www.sagemath.org/packages/experimental/)

-Open a terminal, go to the directory where you have downloaded all
the files of KhovanovSteenrod.  Henceforth, we are assuming that you
are using a Bash shell (the other shells will be similar), and Bash is
configured so that the command "sage" runs the program Sage.
 
-Get the data tables from Knot Atlas.
wget http://katlas.org/Data/Rolfsen.rdf.gz
wget http://katlas.org/Data/Knots11.rdf.gz
wget http://katlas.org/Data/Links.rdf.gz

-Extract the PD-presentations.
zgrep PD_Presentation Rolfsen.rdf.gz > knots.raw
zgrep PD_Presentation Knots11.rdf.gz > knots11.raw
zgrep PD_Presentation Links.rdf.gz > links.raw

-Remove the unknot and the Hopf link. (Due to an unfortunate premature
optimization, the main program main.sage does not work if the link
diagram has an unknot or Hopf link component.)
sed -i 1d knots.raw
sed -i 1d links.raw

-Convert the PD-presentations to our format. (This generates the file
alldata.sage) 
sage convert.sage

-Compute Kh (over F_2) for all prime links up to 11 crossings. (This
generates the file allhom.sage) This can be done in two ways.

--Compute the homology directly; this takes a long time.
sage computehom.sage

--Extract from the Knot Atlas data.
zgrep Integral_Khovanov Rolfsen.rdf.gz > knotshom.raw
zgrep Integral_Khovanov Knots11.rdf.gz > knots11hom.raw
zgrep Integral_Khovanov Links.rdf.gz > linkshom.raw
sed -i 1d linkshom.raw
sage extract.sage

-Compute the action of Sq^1 and Sq^2 on all quantum grading where the
width is at least 3. (This generates the file result.sage)
./batch.sh
This process might take forever, so we recommend using nohup.  
nohup ./batch.sh > /dev/null 2> /dev/null < /dev/null &

-Generate the LaTeX snippet from result.sage
sage texify.sage