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|name|molar_mass|density
47|Ag|silver|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 (4) looks like this:

Table Version (id integer primary key,
               tag text,
               date text,
               notes text);
Table elements (atomic_number integer primary key,
                element text,
                name 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 Coster_Kronig (id integer primary key,
                     element text,
                     initial_level text,
                     final_level text,
                     transition_probability real,
                     total_transition_probability 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 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 Krause_Oliver (id integer primary key,
                     atomic_number integer,
                     element text,
                     edge text,
                     width float);
Table corelevel_widths (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
name	text	English name of element
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 (1995)]. 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 (1974)]. Values are in eV, and each row represents an energy level for an element.

DB Table of Core Hole Widths from Keski-Rahkonen and Krause

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)

Krause_Oliver Table

The Krause_Oliver table holds data for energy widths of the core electronic levels from [Krause and Oliver (1979)]. Values are in eV, and each row represents an energy level for an element.

DB Table of Core Hole Widths from Krause and Oliver

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)

Compton Energies Table

The Compton_energies table holds data for median (90 deg scattering) and mean values of the energies of Compton scattered X-rays, and the mean values of the Compton-scattered electrons as a function of incident X-ray energy. There is only 1 row in this table, with all columns being json-encoded arrays of floats. These values should be finely-spaced enough for linear interpolation

DB Table of Compton-scattered energies.

Column	Type	Description
incident	json_array	Incident X-ray energies (eV)
xray_90deg	json_array	Median scattered X-ray energies (eV)
xray_mean	json_array	Mean scattered X-ray energies (eV)
electron_mean	json_array	Mean scattered electron energies (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 (2000)]. 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)