Using the XrayDB xraydb.sqlite¶
All the data for the X-ray database is held in the SQLite3 file
xraydb.sqlite. To use with SQLite, this file is all you need. While
many programs and languages can access SQLite files, basic
usage with the sqlite3 program (available from Windows, Mac OS X, and
Linux) can be as simple as:
system~> sqlite3 xraydb.sqlite
sqlite> .headers on
sqlite> select * from elements where atomic_number=47;
atomic_number|element|molar_mass|density
47|Ag|107.868|10.48
That is, you can retrieve the data using standard SQL queries built-in to SQLite. Of course, the expectation is that you'd want to use this database within a programming environment. Currently, wrappers exist only for Python.
Overall Database Schema¶
The schema for the SQLite3 database describes where data is held in the database, and how to access it. The schema for the current version (2) looks like this:
TABLE Version (id integer primary key,
tag text,
date text,
notes text);
TABLE elements (atomic_number integer primary key,
element text,
molar_mass real,
density real);
TABLE xray_levels (id integer primary key,
element text,
iupac_symbol text,
absorption_edge real,
fluorescence_yield real,
jump_ratio real);
TABLE xray_transitions (id integer primary key,
element text,
iupac_symbol text,
siegbahn_symbol text,
initial_level text,
final_level text,
emission_energy real,
intensity real);
TABLE photoabsorption (id integer primary key,
element text,
log_energy text,
log_photoabsorption text,
log_photoabsorption_spline text);
TABLE scattering (id integer primary key,
element text,
log_energy text,
log_coherent_scatter text,
log_coherent_scatter_spline text,
log_incoherent_scatter text,
log_incoherent_scatter_spline text);
TABLE Coster_Kronig (id integer primary key,
element text,
initial_level text,
final_level text,
transition_probability real,
total_transition_probability real);
TABLE Waasmaier (id integer primary key,
atomic_number integer,
element text,
ion text,
offset real,
scale text,
exponents text);
TABLE KeskiRahkonen_Krause (id integer primary key,
atomic_number integer,
element text,
edge text,
width float);
TABLE Chantler (id integer primary key,
element text,
sigma_mu real,
mue_f2 real,
density real,
corr_henke float,
corr_cl35 float,
corr_nucl float,
energy text,
f1 text,
f2 text,
mu_photo text,
mu_incoh text,
mu_total text);
More details for each table are given below.
Note
in the tables below the type of json array means that arrays of numerical data are stored in the database as text of JSON-encoded arrays.
Version Table¶
The Version table holds data about the revisions to the database file itself. Each row represents a single revision.
DB Table of Database Versions
Column Type Description id integer counter (primary tag) tag text version name date text date string notes text notes on changes for version
Elements Table¶
The elements table holds basic data about each element. Each row represents an element.
DB Table of Basic Properties of the Elements
Column Type Description atomic_number integer Atomic Number, Z element text Atomic symbol molar_mass float Atomic mass in AMU density float Density of pure element (gr/cm^3)
Xray_Levels Table¶
The xray_levels table holds data for electronic levels of atoms. Each row represents a core electronic level.
DB Table of X-ray and core electronic levels. fluorescence yield gives the probability of an empty level refilling by X-ray fluorescence. The jump ratio is the ratio of values for photo-electric cross section (that is, from Photoabsorption Table) 1 eV above the absorption edge to that 1 eV below the absorption edge. See Table of X-ray Edges
Column Type Description id integer Index (primary key) element text Atomic symbol for element iupac_symbol text IUPAC symbol for level ('K','L3',...) absorption_edge float binding energy for level (eV) fluorescence_yield float fluorescence yield (fraction) jump_ratio float ratio of mu_photo across edge
Xray_Transitions Table¶
The xray_transitions table holds data for transitions between electronic levels of atoms. Each row represents a transition between two levels.
DB Table of X-ray Transitions. Both IUPAC and Siegbahn symbols are given (see Table of X-ray emission lines), as well as the initial and final levels. The intensity is the relative intensity of the transition for a given initial level.
Column Type Description id integer Index (primary key) element text Atomic symbol for element iupac_symbol text IUPAC symbol for transition siegbahn_symbol text Siegbahn symbol for transition initial_level text IUPAC symbol for initial level final_level text IUPAC symbol for final level emission_energy float fluorescence energy (eV) intensity float relative intensity for transition
Photoabsorption Table¶
The photoabsorption table holds data for the photo-electric absorption cross sections in cm^2/gr. Each row represents an element.
DB Table of Photoabsorption Cross Sections. JSON-encoded arrays are held for logs of energy, cross section, and cross section spline (second derivative useful for spline interpolation).
Column Type Description id integer Index (primary key) element text Atomic symbol for element log_energy json array log of Energy values (eV) log_photoabsorption json array log of cross section (cm^2/gr) log_photoabsorption_spline json array log of cross section spline
Scattering Table¶
The scattering table holds data for the coherent and incoherent X-ray scattering cross sections, in cm^2/gr. Each row represents an element.
DB Table of Coherent and Incoherent Scattering Cross Sections. JSON-encoded arrays are held for logs of energy, cross section, and cross section spline (second derivative useful for spline interpolation).
Column Type Description id integer Index (primary key) element text Atomic symbol for element log_energy json array log of Energy values (eV) log_coherent_scatter json array log of cross section (cm^2/gr) log_coherent_scatter_spline json array log of cross section spline log_incoherent_scatter json array log of cross section (cm^2/gr) log_incoherent_scatter_spline json array log of cross section spline
Coster_Kronig Table¶
The Coster_Kronig table holds data for energy levels, partial and total transition probabilities for the Coster-Kronig transitions (Auger processes in which the empty core level is filled from an electron in a higher level with the same principle quantum number). The partial probability describes direct transitions, while the total probability includes cascade effects. Each row represents a transition.
DB Table of Coster-Kronig Transitions.
Column Type Description id integer Index (primary key) element text Atomic symbol for element initial_level text IUPAC symbol for initial level final_level text IUPAC symbol for final level transition_probability float direct transition probability total_transition_probability float total transition probability
Waasmaier Table¶
The Waasmaier table holds data for calculating elastic X-ray scattering factors \(f_0(k)\), from Waasmaier and Kirfel . The scattering factor is unitless, and \(k=\sin(\theta)/\lambda\) where \(\theta\) is the scattering angle and \(\lambda\) is the X-ray wavelength. available for many common ionic states for each element. Each row represents an ion.
DB Table of Elastic Scattering Cross Section Coefficients
Column Type Description id integer Index (primary key) atomic_number integer Atomic Number, Z element text Atomic symbol for element ion text symbol for element and ionization offset float offset value scale json array coefficients for calculation exponents json array coefficients for calculation
KeskiRahkonen_Krause Table¶
The KeskiRahkonen_Krause table holds data for energy widths of the core electronic levels from Keski-Rahkonen and Krause . Values are in eV, and each row represents an energy level for an element.
DB Table of Core Hole Widths
Column Type Description id integer Index (primary key) atomic_number integer Atomic Number, Z element text Atomic symbol for element edge text IUPAC symbol for energy level ('K') width float width of level (eV)
Chantler Table¶
The Chantler table holds data for resonant X-ray scattering factors \(f'(E)\) and \(f''(E)\) as well as photo-electric absorption, coherent, and incoherent scattering factors from Chantler . As with other tables, scattering factors are unitless, and cross sections are in cm^2/gr. Each row represents an element.
DB Table of resonant scattering and mass attenuation coefficients from Chantler.
Column Type Description id integer Index (primary key) element text Atomic symbol for element mue_f2 float factor to convert mu(E) to f''(E) density float atomic density (gr/cm^3) corr_henke float Henke correction to f`(E) corr_cl35 float Cromer-Liberman correction to f`(E) corr_nucl float nuclear correction to f`(E) energy json array energies for interpolation f1 json array f'(E) (e) f2 json array f''(E) (e) mu_photo json array photoabsorption mu(E) (cm^2/gr) mu_incoh json array incoherent scattering (cm^2/gr) mu_total json array total attenuation (cm^2/gr)