[Gausssum-devel] Instructions for using gausssum2

[Noel O'B. <no...@ca...>]

Here is the start of some documentation on gausssum2:


> cclib is the Python package on top of which GaussSum is built. cclib
> does all the hard work of parsing computational chemistry log files,
> performing various related calculations, and also making nice tables
> of the results. GaussSum can be seen as a GUI interface to cclib.
> 
> In other words, everything that GaussSum can do, you can do with
> cclib. This means that you can write programs that extract data from
> logfiles without having to worry about doing the extraction yourself
> for all the different varieties and shapes of logfiles.
> 
> As an example, here is a Python script that uses cclib to find out the
> HOMO of every .log file in the current directory, and print the result
> on the screen.
> 
> from cclib.parsers import G03
> from glob import glob
> 
> for logfile in glob("*.log"):
> 	t = G03(logfile)
> 	t.parse()
> 	print logfile,t.HOMO
> 
> And here's the output in a folder of mine:
> [Insert output here]
> 
> Although you may think that finding the HOMO is a relatively easy task
> and suitable for a command like 'grep', you may forget to consider the
> case for unrestricted calculations, or calculations that involve some
> obscure combination of keywords. The advantage of using a library is
> that it is likely that all possible problems have already been
> discovered due to the large user base. Other parsing tasks are more
> complicated and are completely unsuited to one-line commands, and
> shell scripts.
> 
> So, how does it work? (The following discussion assumes a basic
> knowledge of object-oriented programming)
> 
> In a general sense, you need to create an instance of a subclass of
> the logfile object (the currently available ones are G03, and GAMESS,
> but please add your own favourite program). In the example above, this
> is done by the following statement "t = G03(logfile)".
> 
> Next, call the parse() method of this object. In one pass of the file,
> every useful piece of information is extracted and placed into
> attributes of the object (please add your own extractions too). The
> attributes can be accessed using the dot notation, e.g. t.HOMO
> accesses the extracted information on the HOMO.
> 
> If you want to perform one of the analysis methods present in cclib,
> you need to call one of the 'calc' methods inherited from the
> superclass, for example calcuvspectrum() uses the extracted
> information on electronic transitions to convolute the uvspectrum and
> place the result in t.uvspectrum.
> 
> Finally, if you want to write out information to a file in a
> tab-separated format, you can use one of the 'tidy' methods inherited
> from the superclass, for example tidyevalue() writes out eigenvalue
> information in a nice format along with the names of the molecular
> orbitals.
> 
> And now to specifics.
> 
> Parsing G03 logfiles creates the following attributes (if present in
> the logfile):
> 
> Parsing GAMESS logfiles creates the following attributes (if present
> in the logfile):
> 
> The following 'calc' methods are available:
> 
> The following 'tidy' methods are available:
> 
> Notes for developers:
> (unit testing)