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 (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,
                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

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)

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)