Atomic Data
Any Python model is only as good as the atomic data which goes into making the model. All of the atomic data that Python accepts is read in by the routine get_atomicdata, and all of the data is read in from a series of ascii data files and stored in structures that are defined in atomic.h.
The purpose of documentation is as follows:
to explain the atomic data formats used by Python and the relationship of different sets of data to one another
to explain where the data currently used in Python and to explain how the raw data is translated in to a format the Python accepts
The routines used to translate raw data format (as well as much of the raw data) are contained in a separate github repository These routines are very “rough-and-ready”, and not extensively documented, but so users should beware. On the other hand, they are not exceptionally complicated so in most cases it should be fairly clear from the code what the various routines do.
The “masterfile” that determines what data will be read into Python is determined by the line in the parameter file, which will read something like:
Atomic_data data/standard80.dat
where the file data/standard80.txt will contain names (one to a line) of files which will be read in sequentially. All of the atomic data that comes standardly with Python is stored in the data directory (and its subdirectories) but users are not required to put their data there.
Every line in the atomic data files read by Python consists of a keyword that defines the type of data and various data values that are required for that particular data type. Lines that beging with # or are empty are ignored.
The data from the various files are read as if they were one long file, so how the data is split up into files is a matter of convenience.
However, the data must be read in a logical order. As an simple example, information about elements must be read in prior to information about ions. This allows one to remove all data about, say Si, from a calculation simply by commenting out the line in the atomic data that gives the properties of the element Si, without having to removed all the ion and other information about a data file from the calculation.
The main hierarchy is as follows
Elements
Ions
Energy levels
Lines
Once these sets of data have been read in the order in which other information is read in is irrelevant, that is one can read the collision data (which is indexed to lines) and photoionization cross sections (which are indexed to energy levels) in either order
(Note that although the approach has advantages of allowing one to comment out atoms or ions, it also has the disadvantageby ignoring data, the program does not give you a particularly good summary of what data has been omitted. If concerned about this one should use the advanced command:
@Diag.write\_atomicdata(yes,no)
which prints out an ascii version of the input data that was used.
More information on the various types of input data can be found below: