The Astrophysical Plasma Emission Database (APED)

Within AtomDB, the collection of fundamental atomic data is known as APED. This is data, stored as FITS files, which covers the range of processes required to model the plasma. Each process has its own file, as does each ion, with each file type being denoted by a two letter code.

File types

Ionization and recombination rates
Energy levels and photoionization data
Wavelength and Einstein A values (L is for Lambda, for wavelength)
Electron collisions
Proton collisions
Dielectronic satellite lines
Extra photoionization cross section data, used for imports from XSTAR
Autoionization rates

Filename Conventions

Files are stored within the $ATOMDB/APED directory, with subdirectories for each element and ion. Thus, files relating to Fe XXV (so Fe24+) will be in $ATOMDB/APED/fe/fe_25/ .

Filenames within these directories are made up of 5 parts, in the format [elementsymbol]_[charge+1]_[filetype]_[versionintroduced]_[revisionletter].fits. Thus $ATOMDB/APED/fe/fe_25/fe_25_LV_v3_0_0_a.fits is the Fe XXV energy level file, introduced in version 3_0_0 and still on its first revision ('a'). Revision number is rarely updated, it is only for correction of errors. More typically a new version of the file is introduced (so v3_0_0 becomes v3_0_9 or some such) instead.

Note that historically files were named by the author of the data within them, however this became untenable as data from multiple sources were incorporated into each file. However as a result there are some older files where, instead of a version number, there is a 3 letter abbreviation of the author's initials instead. These files are old, but often still in use, e.g. for proton excitation collisions.

In addition, we store some files outside this structure for a combination of historic and convenience reasons. Within the APED directory, there are two further subdirectories. The "ionbal" directory stores the equilibrium ionization balance from each release of AtomDB. Again, this file is only updated when this changes so there isn't always a 1-1 correlation between releases and versions. Within the "ionbal" directory there is also an "eigen" subdirectory, which includes eigenvectors for solving non-equilibrium ionization balance calculations.

Finally, in the misc folder, abundance files are stored. These list the elemental abundance for a range of different data sets for the elements from hydrogen (Z=1) to zinc (Z=30).

Accessing the Data

In days gone by, the AtomDB database could be downloaded directly. However, it has now grown to an unreasonable size for such distribution, so we have implemented an on-demand access method through a python interface, pyatomdb. Full details can be found on the project website, but in short, by issuing a command such as pyatomdb.atomdb.get_data(26, 25, 'LV'), the Fe XXV energy level file will be retrieved and stored on your hard disk, where it can be interrogated using python or any FITS file viewer, such as FV.

File Formats

All files are stored as FITS binary files. They are all different due to the needs of different datatypes: in AtomDB we strive to record the data in as close to the original format as possible (without adding interpolation or analytic approximations to the published data) which means we have to be flexible to handle a range of possible formats within a single data type. There are a python helper routines within pyatomdb which will allow you to extract rate coefficients and so on if desired. However, for the raw data formats, see the following two publications:

Smith et al 2001
LV, LA, EC, PC and DR files
Foster et al 2017
IR, PI, AI files files

Which Files to Access?

There are numberous different files for each ion and each process, reflecting updates to the data over time. To find which dataset was used in a previous release of AtomDB, one can look at the filemap file (e.g. filemap_v3.0.6) for each release. This lists every file which was used by the APEC code to create emissivity files.

Within pyatomdb, the file retreived by get_data will always be the one for the current version of the database. If you want to look at older versions, the pyatomdb.util.switch_version('\') command can be used to set the database to older data.