PyAtomDB & AtomDB

The AtomDB Project consists of a large atomic database designed for creating spectra of collisionally excited plasmas in the UV and X-ray wavebands for use in astronomy and astrophysics research. It has been successfully used for some time within several different spectral analysis suites, such as XSPEC and Sherpa.

There are two main parts to AtomDB:

The Astrophysical Plasma Emission Database (APED)

A series of FITS files which store the atomic data necessary for modelling emission from collisional plasmas from elements from H through to Zn.

The Astrophysical Plasma Emission Code (APEC)

Code which takes the APED and uses it to model a collisional plasma, creating emissivity files for line and continuum emission. These output files are then used in a range of models such as the apec, nei and pshock models amongst others.

Starting in 2015, PyAtomDB was developed to achieve a number of goals:

1. To replace the APEC code (formerly in C) with a more flexible tool for larger data sets

2. To allow interactive user access to the underlying database, which was always freely available but sometimes difficult to use

3. To enable creating more flexible spectra based on the outputs of AtomDB

4. To enhance the types of spectra which can be modeled in AtomDB, and astronomer interaction with these models

5. To facililtate inclusion of AtomDB models in other software (often python based).

Contents

• Installation
  • ATOMDB Directory
  • Usage Data Collection
• PyAtomDB Example Scripts
  • Module Structure
  • Spectra
    • CIESession Class
      • Making a Spectrum
      • Handling Large Response Matrices
      • Line Broadening
      • Changing Abundances
      • Return line list
      • Return line emissivity
    • NEISession Class
      • Making a Spectrum
      • Making a Linelist
  • Getting Atomic Data
    • Getting Rate Coefficients
  • Calculating Plasma Conditions
    • Getting Charge State Distribution
  • Including APEC models in PyXSPEC
  • Resonant Scattering (rsapec) model
    • Example script using rsapec model in PyXSPEC
  • Individual Use Cases
    • Get PI Cross Sections
    • Make Cooling Curve
• Module Documentation
  • apec module
    • calc_brems_gaunt()
    • calc_cascade_population()
    • calc_ee_brems()
    • calc_full_ionbal()
    • calc_ioniz_popn()
    • calc_recomb_popn()
    • calc_satellite()
    • calc_total_coco()
    • compress_continuum()
    • continuum_append()
    • create_chdu_cie()
    • create_cparamhdu_cie()
    • create_lhdu_cie()
    • create_lhdu_nei()
    • create_lparamhdu_cie()
    • do_brems()
    • do_lines()
    • extract_gauntff()
    • gather_rates()
    • generate_apec_headerblurb()
    • generate_cie_outputs()
    • generate_datatypes()
    • generate_nei_outputs()
    • kurucz()
    • make_vector()
    • make_vector_nbins()
    • parse_par_file()
    • return_ionbal()
    • run_apec()
    • run_apec_element()
    • run_apec_ion()
    • run_wrap_run_apec()
    • solve_ionbal()
    • solve_level_pop()
    • wrap_ion_directly()
    • wrap_run_apec()
    • wrap_run_apec_element()
    • wrap_update_one_ion()
  • atomic module
    • Z_to_mass()
    • Ztoelname()
    • Ztoelsymb()
    • config_to_occup()
    • elsymb_to_Z()
    • elsymb_to_z0()
    • get_maxn()
    • get_parity()
    • int2roman()
    • int_to_roman()
    • occup_to_cfg()
    • occup_to_config()
    • parse_config()
    • parse_eissner()
    • roman_to_int()
    • shorten_config()
    • spectroscopic_name()
    • spectroscopictoz0()
    • z0_to_mass()
    • z0toelname()
    • z0toelsymb()
  • atomdb module
    • calc_rad_rec_cont()
    • calc_rrc()
    • calc_two_phot()
    • format_level()
    • get_abundance()
    • get_data()
    • get_filemap_file()
    • get_ionpot()
    • get_ionrec_rate()
    • get_maxwell_rate()
    • get_oscillator_strength()
    • make_lorentz()
    • read_filemap()
    • rrc_ph_value()
    • sigma_photoion()
    • write_filemap()
  • const module
  • spectrum module
    • CIESession
      • CIESession.format_linelist()
      • CIESession.return_line_emissivity()
      • CIESession.return_linelist()
      • CIESession.return_spectrum()
      • CIESession.set_abund()
      • CIESession.set_abundset()
      • CIESession.set_broadening()
      • CIESession.set_eebrems()
      • CIESession.set_response()
    • CIESession_RS
      • CIESession_RS.format_linelist()
      • CIESession_RS.return_line_emissivity()
      • CIESession_RS.return_linelist()
      • CIESession_RS.return_spectrum()
      • CIESession_RS.set_abund()
      • CIESession_RS.set_abundset()
      • CIESession_RS.set_broadening()
      • CIESession_RS.set_eebrems()
      • CIESession_RS.set_response()
    • NEISession
      • NEISession.format_linelist()
      • NEISession.return_line_emissivity()
      • NEISession.return_linelist()
      • NEISession.return_spectrum()
      • NEISession.set_abund()
      • NEISession.set_abundset()
      • NEISession.set_broadening()
      • NEISession.set_eebrems()
      • NEISession.set_response()
    • PShockSession
      • PShockSession.format_linelist()
      • PShockSession.return_line_emissivity()
      • PShockSession.return_linelist()
      • PShockSession.return_spectrum()
      • PShockSession.set_abund()
      • PShockSession.set_abundset()
      • PShockSession.set_broadening()
      • PShockSession.set_eebrems()
      • PShockSession.set_response()
    • calc_ee_brems_spec()
  • util module
    • NotImplementedError
      • NotImplementedError.add_note()
      • NotImplementedError.args
      • NotImplementedError.with_traceback()
    • OptionError
      • OptionError.add_note()
      • OptionError.args
      • OptionError.with_traceback()
    • ReadyError
      • ReadyError.add_note()
      • ReadyError.args
      • ReadyError.with_traceback()
    • UnitsError
      • UnitsError.add_note()
      • UnitsError.args
      • UnitsError.with_traceback()
    • check_version()
    • convert_spec()
    • convert_temp()
    • download_atomdb_emissivity_files()
    • download_atomdb_nei_emissivity_files()
    • figcoords()
    • generate_equilibrium_ionbal_files()
    • generate_isis_files()
    • generate_web_fitsfiles()
    • generate_xspec_ionbal_files()
    • initialize()
    • keyword_check()
    • load_user_prefs()
    • make_linelist()
    • make_release_filetree()
    • make_release_tarballs()
    • make_vec()
    • md5Checksum()
    • mkdir_p()
    • question()
    • record_upload()
    • switch_version()
    • unique()
    • write_ai_file()
    • write_develop_data()
    • write_dr_file()
    • write_ec_file()
    • write_ionbal_file()
    • write_ir_file()
    • write_la_file()
    • write_lv_file()
    • write_user_prefs()
• License
• Contact

Outline

PyAtomDB is a selection of utilities designed to interact with the AtomDB database . These utilities are under constant development. Please get in touch with any issues that arise.

There are several different modules currently. These are:

atomdb

A series of codes for interacting with the AtomDB atomic database

atomic

Basic atomic data routines - e.g. converting element symbols to atomic number, etc.

const

Physical and code related constants

spectrum

Routines for generating spectra from the published AtomDB line and continuum emissivity files

util

Utility codes (sorting etc) that pyatomdb relies on.

apec

The full APEC code

To report bugs or make feature requests, email the code authors or raise an issue at the github page

Indices and tables

• Index

• Module Index

• Search Page