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The wayback machine to the rescue

with 7 comments

Years ago I made some on-line material available on my (old) website in order to supplement some of my publications. In the meantime I have closed down the old website, and guess what, now the material has been requested (cough!). What to do now? Use the the internet archive/waybackmachine.
“Browse through over 150 billion web pages archived from 1996 to a few months ago. To start surfing the Wayback, type in the web address of a site or page where you would like to start, and press enter. Then select from the archived dates available. The resulting pages point to other archived pages at as close a date as possible. Keyword searching is not currently supported.”

The material which is related to some publications in Applied Catalysis and the Linux Gazette. The material in question can be found here, and is even shown below:

Supplementary material

From Andr

This page contains supplementary material to some of my publications

Table of contents [showhide]

Linux gazette 114

In order to try out Example 3 in the article Python for scientific use. Part I: Data visualization in Linux Gazette 114 (2005) (http://linuxgazette.net/114/andreasen.html) a number of data files are needed.

These data files are contained within the 3ddata.tar.gz (http://andr.dk/lg114/3ddata.tar.gz) file. In order to extract all datafiles do:

  tar xvfz 3ddata.tar.gz

in the directory from which the python script is run.

Linux gazette 115

In order to try out Example 3 in the article Python for scientific use. Part II: Data analysis in Linux Gazette 115 (2005) (http://linuxgazette.net/115/andreasen.html) a number of data files are needed.

These data files are contained within the 3dtdata.tar.gz (http://andr.dk/lg115/3dtdata.tar.gz) file. In order to extract all datafiles do:

  tar xvfz 3dtdata.tar.gz

in the directory from which the python script is run.

Octave files

The kinetic models published in Simplified kinetic models of methanol oxidation on silver are all implemented in a number of octave (http://www.octave.org) scripts. You can see all individual files in the table below. All files can be obtained either by downloading octavefiles.tar.gz (http://andr.dk/octavefiles/octavefiles.tar.gz) or by

  wget -i FILELIST.txt

from the directory to which the files should be downloaded. First, download the FILELIST (http://andr.dk/octavefiles/FILELIST.txt).

List of octave files
File name Description
MeOH_test.m (http://andr.dk/octavefiles/MeOH_test.m) Main file
Keqsel.m (http://andr.dk/octavefiles/Keqsel.m) Reaction step equilibrium constants calculated using statistical thermodynamics
K_HandS.m (http://andr.dk/octavefiles/K_HandS.m) Reaction step equilibrium constants calculated using enthalpies and entropies
fullrateorig.m (http://andr.dk/octavefiles/fullrateorig.m) The original rate law from quasi equilibrium approximation and stat. therm. with a plug-flow reactor model included
fullrate.m (http://andr.dk/octavefiles/fullrate.m) The original rate law from quasi equilibrium approximation and classical thermodynamics with a plug-flow reactor model included
marirate.m (http://andr.dk/octavefiles/marirate.m) The MARI approximation
israte.m (http://andr.dk/octavefiles/israte.m) The IS approximation
powerlawrate.m (http://andr.dk/octavefiles/powerlawrate.m) The clean surface approximation
qtransA.m (http://andr.dk/octavefiles/qtransA.m) Calculation of the translational partition function
qvibA.m (http://andr.dk/octavefiles/qvibA.m) Calculation of the vibrational partition function for a single vibration (cm-1)
qvibAJ.m (http://andr.dk/octavefiles/qvibAJ.m) Calculation of the vibrational partition function for a single vibration (J/mol)
qrotA2D.m (http://andr.dk/octavefiles/qrotA2D.m) Calculation of the 2-D rotational partition function (cm-1)
qrotA2DJ.m (http://andr.dk/octavefiles/qrotA2DJ.m) Calculation of the 2-D rotational partition function for a single vibration (J/mol)
qrotA3D.m (http://andr.dk/octavefiles/qrotA3D.m) Calculation of the 3-D rotational partition function (cm-1)
qvibtotA.m (http://andr.dk/octavefiles/qvibtotA.m) Calculation of the total vibrational partition function for a molecule (cm-1)
HvibA.m (http://andr.dk/octavefiles/HvibA.m) Calculation of the vibrational enthalpy of a single vibration (cm-1)
HvibAJ.m (http://andr.dk/octavefiles/HvibAJ.m) Calculation of the vibrational enthalpy of a single vibration (J/mol)
HvibtotA.m (http://andr.dk/octavefiles/HvibtotA.m) Calculation of the total vibrational enthalpy for a molecule (cm-1)

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Written by aandreasen

September 29, 2010 at 9:28 am

7 Responses

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  1. Hello, Anders Andreasen
    It was me who asked editor of LG for your 3D data. I have found this web site and downloaded the files.
    Thank you.
    The problem now is that the scripts do not work.
    1st script error:
    NameError: name ‘io’ is not defined
    WARNING: Failure executing file:
    2nd script error:
    NameError: name ‘Float’ is not defined
    WARNING: Failure executing file:
    Could you, please, help me get these script running?

    Dima

    October 3, 2010 at 5:13 am

    • The “io” relates to the scipy package. Do you have that installed? It works fine on my computer. The “Float” issue is probably due to changes in puthon/scipy try “float” instead.

      Anders

      aandreasen

      October 3, 2010 at 7:37 am

      • Another thing. My examples uses the “gplt” module for plotting, which is obsolete, and heavily replaced by matplotlib instead, so that part may not work properly either.

        aandreasen

        October 3, 2010 at 7:38 am

  2. scipy is installed.
    I have copied this lline ‘import scipy.io.array_import’ from ‘lgtixrpd.py’, but with no success. Just no go. What does it do? May be I can replace it some how? Any suggestion?
    I replace ‘Float’ with ‘float’ everywhere in both scripts, and now ‘lgtixrpd.py’ gives me this:
    sh: ggv: not found
    pstopnm: Writing ppmraw file
    /usr/lib/python2.6/dist-packages/numpy/lib/utils.py:108: DeprecationWarning: read_array is deprecated
    warnings.warn(str1, DeprecationWarning)
    /usr/lib/wingide-101-3.2/src/debug/tserver/_sandbox.py:27: DeprecationWarning: os.popen3 is deprecated. Use the subprocess module.
    Processing file nr.: 0 of 76 with failure
    Processing file nr.: 1 of 76 with failure
    Processing file nr.: 2 of 76 with succes

    Processing file nr.: 74 of 76 with failure
    Processing file nr.: 75 of 76 with failure
    Status: 32512
    Status: 0
    Any ideas how I can get your scripts working? I would be very grateful for your help, I’m new in python.
    Thanks.

    Dima

    October 3, 2010 at 11:02 pm

    • Hi, Anders
      The 1st problem with ‘3ddata_1.py’ was solved: import scipy.io.array_import + scipy.io.array_import.read_array. It generates one figure with 3D data.
      There is a warning, however:
      “/usr/lib/python2.6/dist-packages/numpy/lib/utils.py:108: DeprecationWarning: read_array is deprecated
      warnings.warn(str1, DeprecationWarning)”
      I’ll explore this script, and try to solve the 2nd problem.
      Your help is very much appreciated.
      Dima

      Dima

      October 4, 2010 at 12:42 am

  3. I got them running!
    Now I have to understand how it works line by line, and then replace somehow ‘gnuplot’ with ‘matplotlib’.
    Also those methods ‘read_array’ and ‘os.popen3’ seem to be deprecated. I guess they have to be replace with newer methods too.
    Thanks a lot, Anders.
    If you have some suggestions, helpful material, etc, I’m open for all that.
    Dima

    Dima

    October 4, 2010 at 4:00 am

  4. you can use read_array anyway for now, although it will probably be removed in future versions of scipy. There are alternatives see e.g. http://www.scipy.org/Cookbook/InputOutput. Regarding os.popen, this you’ll not need for plotting with matplotlib. Matplotlib is way easier, very similar to matlab. See e.g. http://www.scipy.org/Cookbook/Matplotlib

    aandreasen

    October 4, 2010 at 10:31 am


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