xtotdam / leipzig-report

Leipzig report

This tool helps to visualize and understand the data, which was obtained during the experiments at Laser Labor at TROPOS in Leipzig.

Dependencies

• Latex with a number of packages
• Python 2
  • numpy
  • scipy
  • matplotlib

What it needs

All the original data goes to data.txt or how would you like to call it in arrhenuis/ folder (NB! it is arrhenUIs). Name of this file will be given as argument to arrhenius.py, who will do almost all the work. Passing the name can be omitted, then it will be default to data.txt.

Data format and limitations are explained in data.txt.

See make gendata below if no data.txt is presented.

Output

For every compound mentioned in data.txt following LaTeX parts for the resulting document will be produced. There * is acronym for any compound, given in data.txt.

• *-table.tex A table with original data for both pH and already calculated rate constants for acid and anion forms, this is based on given pKa.
• *-fractions.tex A plot of fractions of acid and anion parts at different pH. Also a table with two fractions at used pH is provided, which can be omitted (see arrhenius.py, function fractions()).
• *-data.tex Heart of the tool. A table with Arrhenius and thermodynamic data for both pH, calculated with another reincarnation of Prof. Dr. H. Herrmann's code.
• *-split.tex A set of two equations for acid and anion rate constants, calculated based on pH and Arrhenius data.
• *-pure.tex Arrhenius and thermodynamic data for already splitted rate constants.
• *-sigma-table.txt Little tables to copy-paste into SigmaPlot. 6 columns are generated: T, 1/T, lg(k), lg(k-error), lg(k+error), lg(error).

A nice Arrhenius plot with original and calculated data is generated, named *.double.pdf. (Generating png image is based on bool flag, see arrhenius.py, A bit of settings in the beginning of file)

Also a plot of acid/anion fractions is generated, named *.fractions.pdf.

You can generate fractions plots for using exceptions.py. It was created for compounds with very low rate constant and provides only *-fractions.tex and *.fractions.pdf.

Final table with various termodynamic data, termodyn.tex, is generated by termodyn.py, which uses data, generated by arrhenius.py: termodyn-acid.data.txt and termodyn-anion.data.txt.

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Nothing in main-leipzig.tex is generated automatically, it just uses arrhenius.py's outputs, because you never know what data you will have to present in addition to mentioned above and what text you will write for all the numbers and graphs.

Launching

Windows

Just launch compile.cmd in the root directory

To delete old files launch clean.cmd

Linux + Windows with make etc

make all to compile everything

make latex to compile latex document only

make clean to delete temporary files

make gendata to generate junk data file, which also explains his own format

make purge = make clean + remove data.txt

Also try running python arrhenuis/arrhenius.py -h for some information on maybe useful arguments

License

MIT License, except for hh.py, which is published under separate license.

TODO

• describe exceptions.py
• describe termodyn.py
• ask HH about license
• receive answer
• code commentary
• license
• rewrite linear regression using scipy / OLS from MR