XrayDB

https://github.com/xraypy/xraydb
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XrayDB provides atomic data, characteristic X-ray energies, and X-ray cross sections for the...
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### Install XrayDB via pip

Source: https://github.com/xraypy/xraydb/blob/master/doc/installation.rst

Use this command to install the XrayDB Python module and its associated SQLite database.

```bash
pip install xraydb
```

--------------------------------

### Calculate Fluxes for Gas Mixtures

Source: https://github.com/xraypy/xraydb/blob/master/doc/examples.rst

Example of specifying a gas mixture using a dictionary of gas names and fractional densities.

```python
>>> fl = ionchamber_fluxes(gas={'Kr':0.5, 'Ar': 0.5}, volts=1.25,
                           energy=18000, length=10,
                           sensitivity=1, sensitivity_units='microA/V')
>>> print(f"Incident= {fl.incident:g} Hz, Transmitted flux= {fl.transmitted:g} Hz")
Incident= 1.43737e+10 Hz, Transmitted flux= 3.28986e+09 Hz
```

--------------------------------

### Calculate Ion Chamber Currents Example

Source: https://github.com/xraypy/xraydb/blob/master/doc/examples.rst

Basic usage example for calculating incident and transmitted flux for a nitrogen-filled chamber.

```python
>>> fl = ionchamber_fluxes(gas='nitrogen', volts=1.25, energy=18000,
                               length=10.0, sensitivity=1.e-6)
>>> print(f"Incident= {fl.incident:g} Hz, Transmitted flux= {fl.transmitted:g} Hz")
Incident= 2.2358e+12 Hz, Transmitted flux= 2.214e+12 Hz
```

--------------------------------

### XrayDB Python API Usage

Source: https://github.com/xraypy/xraydb/blob/master/doc/python.rst

Examples of using xraydb functions for atomic properties, scattering factors, emission lines, absorption edges, and attenuation factors.

```pycon
>>> import xraydb
>>> xraydb.atomic_number('Ag')
47
#
# X-ray elastic (Thomson) scattering factors:
>>> import numpy as np
>>> q =np.linspace(0, 5, 11)
>>> xraydb.f0('Fe', q)
array([25.994603  , 11.50848469,  6.55945765,  4.71039413,  3.21048827,
       2.20939146,  1.65112769,  1.36705887,  1.21133507,  1.10155689,
       1.0035555 ])
#
# X-ray emission lines:
>>> for name, line in xraydb.xray_lines('Zn', 'K').items():
...     print(name, ' = ', line)
...
Ka3  =  XrayLine(energy=8462.8, intensity=0.000316256, initial_level='K', final_level='L1')
Ka2  =  XrayLine(energy=8614.1, intensity=0.294353, initial_level='K', final_level='L2')
Ka1  =  XrayLine(energy=8637.2, intensity=0.576058, initial_level='K', final_level='L3')
Kb3  =  XrayLine(energy=9567.6, intensity=0.0438347, initial_level='K', final_level='M2')
Kb1  =  XrayLine(energy=9570.4, intensity=0.0846229, initial_level='K', final_level='M3')
Kb5  =  XrayLine(energy=9648.8, intensity=0.000815698, initial_level='K', final_level='M4,5')
#
# X-ray absorption edges:
>>> xraydb.xray_edge('As', 'K')
XrayEdge(energy=11867.0, fyield=0.548989, jump_ratio=7.314)
#
# X-ray attenuation factors:
>>> as_kedge = xraydb.xray_edge('As', 'K').energy
>>> energies = np.linspace(-50, 50, 5) + as_kedge
>>> muvals = xraydb.mu_elam('As', energies)
>>> for en, mu in zip(energies, muvals):
...     print("{:.0f}   {:8.2f}".format(en, mu))
...
11817      26.07
11842      25.92
11867      25.77
11892     178.32
11917     177.38
```

--------------------------------

### Get material properties

Source: https://github.com/xraypy/xraydb/blob/master/doc/python.rst

Retrieves the chemical formula and density for a specified material name.

```pycon
>>> xraydb.get_material('kapton')
('C22H10N2O5', 1.43)
```

--------------------------------

### Initialize XrayDB Instance

Source: https://github.com/xraypy/xraydb/blob/master/doc/python.rst

Use this to obtain an instance of the XrayDB object for accessing database methods.

```pycon
>>> import xraydb
>>> xdb = xraydb.get_xraydb()
```

--------------------------------

### Clone XrayDB Repository

Source: https://github.com/xraypy/xraydb/blob/master/doc/installation.rst

Use this command to download the full source code kit for development purposes.

```bash
git clone https://github.com/xraypy/XrayDB.git
```

--------------------------------

### Querying XrayDB with SQLite

Source: https://github.com/xraypy/xraydb/blob/master/doc/dbschema.rst

Basic command-line usage for accessing the database and executing SQL queries.

```default
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
```

--------------------------------

### coated_reflectivity(coating, coating_thick, substrate, theta, energy, coating_dens=None, surface_roughness=0.0, substrate_dens=None, substrate_roughness=0.0, binder=None, binder_thick=None, binder_dens=None, polarization='s', output='intensity')

Source: https://github.com/xraypy/xraydb/blob/master/doc/python.rst

Calculates the reflectivity for a coated mirror.

```APIDOC
## coated_reflectivity

### Description
Calculates the reflectivity for a coated mirror given the coating and substrate properties.

### Parameters
- **coating** (str) - Required - Coating material name or formula.
- **coating_thick** (float) - Required - Thickness of coating in Angstroms.
- **substrate** (string) - Required - Substrate material name or formula.
- **theta** (float or nd-array) - Required - Mirror angle in radians.
- **energy** (float or nd-array) - Required - X-ray energy in eV.
- **coating_dens** (None) - Optional - Density of mirror coating in g/cm^3.
- **surface_roughness** (float) - Optional - Coating roughness in Angstroms.
- **substrate_dens** (float) - Optional - Density of substrate in g/cm^3.
- **substrate_roughness** (float) - Optional - Substrate roughness in Angstroms.
- **binder** (str) - Optional - Binder material name or formula.
- **binder_thick** (float) - Optional - Thickness of binder in Angstroms.
- **binder_dens** (float) - Optional - Density of binder in g/cm^3.
- **polarization** ('s' or 'p') - Optional - Mirror orientation relative to X-ray polarization.
- **output** (str) - Optional - Output intensity or complex amplitude.

### Returns
- **reflectivity** (float/array) - Mirror reflectivity values.
```

--------------------------------

### multilayer_reflectivity(stackup, thickness, substrate, theta, energy, n_periods=1, density=None, substrate_density=None, substrate_rough=0.0, surface_rough=0.0, polarization='s', output='intensity')

Source: https://github.com/xraypy/xraydb/blob/master/doc/python.rst

Calculates the reflectivity for a multilayer mirror.

```APIDOC
## multilayer_reflectivity

### Description
Calculates the reflectivity for a multilayer mirror based on the provided stackup, thickness, and material properties.

### Parameters
- **stackup** (list of formulas) - Required - Material name or formula (e.g., 'Si', 'Rh').
- **thickness** (list) - Required - Thickness of layers in Angstroms.
- **substrate** (string) - Required - Substrate material name or formula.
- **theta** (float or nd-array) - Required - Mirror angle in radians.
- **energy** (float or nd-array) - Required - X-ray energy in eV.
- **n_periods** (int) - Optional - Number of periods in multilayer.
- **density** (list or None) - Optional - Material densities in g/cm^3.
- **substrate_density** (float) - Optional - Density of substrate in g/cm^3.
- **substrate_rough** (float) - Optional - Mirror roughness in Angstroms.
- **surface_rough** (float) - Optional - Mirror roughness in Angstroms.
- **polarization** ('s' or 'p') - Optional - Mirror orientation relative to X-ray polarization.
- **output** (str) - Optional - Output intensity or complex amplitude.

### Returns
- **reflectivity** (float/array) - Mirror reflectivity values.
```

--------------------------------

### ck_probability(element, initial, final, total=True)

Source: https://github.com/xraypy/xraydb/blob/master/doc/python.rst

Calculates the transition probability for an element given the initial and final levels.

```APIDOC
## ck_probability(element, initial, final, total=True)

### Description
Retrieves the transition probability for an element between specified initial and final levels.

### Parameters
- **element** (int, str) - Required - Atomic number or atomic symbol for the element.
- **initial** (str) - Required - IUPAC symbol for the initial level.
- **final** (str) - Required - IUPAC symbol for the final level.
- **total** (bool) - Optional - Whether to include transitions via possible intermediate levels (default: True).

### Returns
- **float** - Transition probability, or 0 if the transition is not allowed.
```

--------------------------------

### Calculate Ion Chamber Fluxes with Different Sensitivity Units

Source: https://github.com/xraypy/xraydb/blob/master/doc/examples.rst

Demonstrates equivalent results using different sensitivity unit specifications.

```python
>>> fluxes = ionchamber_fluxes('N2', volts=1, energy=10000, length=10,
                               sensitivity=1.e-9)
>>> fluxes = ionchamber_fluxes('N2', volts=1, energy=10000, length=10,
                               sensitivity=1, sensitivity_units='nA/V')
```

--------------------------------

### Retrieve materials list

Source: https://github.com/xraypy/xraydb/blob/master/doc/python.rst

Fetches all available materials from the database, optionally filtered by category.

```pycon
>>> for name, m in xraydb.get_materials().items():
...      print(name, m)
...
water H2O 1.0
lead Pb 11.34
aluminum Al 2.7
kapton C22H10N2O5 1.42
polyimide C22H10N2O5 1.42
nitrogen N 0.00125
argon Ar 0.001784
...
```

--------------------------------

### Calculate absorption for specific materials

Source: https://github.com/xraypy/xraydb/blob/master/doc/examples.rst

Demonstrates replacing the default material calculation with a specific material and density.

```python
mu = material_mu('H2O', energy)
```

```python
mu = material_mu('CaCO3', energy, density=2.71)
```

--------------------------------

### Find material instance

Source: https://github.com/xraypy/xraydb/blob/master/doc/python.rst

Looks up a material by name or formula and returns the corresponding Material instance.

```pycon
>>> xraydb.find_material('kapton')
Material(formula='C22H10N2O5', density=1.42, name='kapton', categories=['polymer'])
```

--------------------------------

### get_materials(force_read=False, categories=None)

Source: https://github.com/xraypy/xraydb/blob/master/doc/python.rst

Retrieves a dictionary of all available materials from the database.

```APIDOC
## get_materials(force_read=False, categories=None)

### Description
Fetches all materials currently stored in the database.

### Parameters
- **force_read** (bool) - Optional - Whether to force a re-reading of the materials database. Defaults to False.
- **categories** (list of strings) - Optional - Restrict results to those matching specific category names.

### Returns
- **dict** - A dictionary with material names as keys and Materials instances as values.
```

--------------------------------

### Draw Energy Levels and Transitions

Source: https://github.com/xraypy/xraydb/blob/master/poster/elines.tex

Path commands defining the horizontal energy levels and vertical transition lines with labels.

```latex
(0, 0mm) node[edge]$K$ -- ++(29, 0) node[orbital] $1s$;
 (0, 40mm) node[edge]$L_1$ -- ++(29, 0) node[orbital] $2s$;
 (0, 45mm) node[edge]$L_2$ -- ++(29, 0) node[orbital] $2p_{1/2}$;
 (0, 50mm) node[edge]$L_3$ -- ++(29, 0) node[orbital] $2p_{3/2}$;

 (0, 80mm) node[edge] $M_1$ -- ++(29, 0) node[orbital] $3s$;
 (0, 85mm) node[edge] -- ++(29, 0) node[orbital] $3p_{1/2}$;
 (0, 90mm) node[edge] $M_3$ -- ++(29, 0) node[orbital] $3p_{3/2}$;
 (0, 95mm) node[edge] -- ++(29, 0) node[orbital] $3d_{3/2}$;
 (0, 100mm) node[edge] $M_5$ -- ++(29, 0) node[orbital] $3d_{5/2}$;

 (0, 120mm) node[edge] $N_1$ -- ++(29, 0) node[orbital] $4s$;
 (0, 125mm) node[edge] -- ++(29, 0) node[orbital] $4p_{1/2}$;
 (0, 130mm) node[edge] $N_3$ -- ++(29, 0) node[orbital] $4p_{3/2}$;
 (0, 135mm) node[edge] -- ++(29, 0) node[orbital] $4d_{3/2};
 (0, 140mm) node[edge] $N_5$ -- ++(29, 0) node[orbital] $4d_{5/2};
 (0, 145mm) node[edge] -- ++(29, 0) node[orbital] $4f_{5/2};
 (0, 150mm) node[edge] $N_7$ -- ++(29, 0) node[orbital] $4f_{7/2};


 (5mm, 152mm) -- ++(5mm, -7mm);
 (10mm, 147mm) -- node[sieg] $M_{\alpha}$ (10mm, 120mm) -- (10mm, 100mm) ;
 (25mm, 147mm) -- node[sieg] $M_{\beta}$ (25mm, 97mm) -- (25mm, 95mm) ;


 (35mm, 82mm) -- node[sieg] $L_l$ (35mm, 62mm) -- node[frac] 0.003 (35mm, 50mm) ;
 (50mm, 97mm) -- node[sieg] $L_{\alpha_2}$ (50mm, 64mm) -- node[frac] 0.09 (50mm, 50mm) ;
 (65mm, 102mm) -- node[sieg] $L_{\alpha_1}$ (65mm, 69mm) -- node[frac] 0.80 (65mm, 50mm) ;

 (75mm, 142mm) -- (80mm, 135mm);
 (80mm, 137mm) -- node[sieg] $L_{\beta_2}$ (80mm, 77mm) -- node[frac] 0.11 (80mm, 50mm) ;


 (105mm, 97mm) -- node[sieg] $L_{\beta_1}$ (105mm, 58mm) -- node[frac] 0.88 (105mm, 45mm) ;
 (120mm, 137mm) -- node[sieg] $L_{\gamma_1}$ (120mm, 69mm) -- node[frac] 0.09 (120mm, 45mm) ;


 (145mm, 87mm) -- node[sieg] $L_{\beta_4}$ (145mm, 55mm) -- node[frac] 0.32 (145mm, 40mm) ;
 (160mm, 92mm) -- node[sieg] $L_{\beta_3}$ (160mm, 61mm) -- node[frac] 0.50 (160mm, 40mm) ;
 (175mm, 127mm) -- node[sieg] $L_{\gamma_2}$ (175mm,67mm) -- node[frac] 0.08 (175mm, 40mm) ;
 (190mm, 132mm) -- node[sieg] $L_{\gamma_3}$ (190mm, 79mm) -- node[frac] 0.10 (190mm, 40mm) ;


 (215mm, 47mm) -- node[sieg] $K_{\alpha_2}$ (215mm, 16mm) -- node[frac] 0.29 (215mm, 0mm) ;
 (230mm, 52mm) -- node[sieg] $K_{\alpha_1}$ (230mm, 23mm) -- node[frac] 0.54 (230mm, 0mm) ;
 (245mm, 87mm) -- node[sieg] $K_{\beta_3}$ (245mm, 30mm) -- node[frac] 0.05 (245mm, 0mm);
 (260mm, 92mm) -- node[sieg] $K_{\beta_1}$ (260mm, 36mm) -- node[frac] 0.09 (260mm, 0mm);

 (270mm, 132mm) -- ++(5mm, -7mm);
 (275mm, 127mm) -- node[sieg] $K_{\beta_2}$ (275mm, 48mm) -- node[frac] 0.03 (275mm, 0mm) ;
```

--------------------------------

### Calculate coated mirror reflectivity

Source: https://github.com/xraypy/xraydb/blob/master/doc/examples.rst

Uses coated_reflectivity to model mirrors with specific coating and binding layers, comparing them against bulk material reflectivity.

```python
import numpy as np
from xraydb import (coated_reflectivity, mirror_reflectivity)
import matplotlib.pyplot as plt

coating = 'Rh'
coating_thick = 300
substrate = 'Si'
theta = 0.004
energy = np.linspace(10000, 35000, 500)
binder = 'Cr'
binder_thick = 30

refl_coat = coated_reflectivity(coating, coating_thick, substrate, theta, energy, binder=binder, binder_thick=binder_thick)
refl_rhod = mirror_reflectivity('Rh', theta, energy)

title = f'$\rm {coating_thick} \AA \> {coating}/{binder_thick} \AA \> {binder} \> coated \> {substrate} \> mirror \> \theta\, =\, {theta*1000:.0f} mrad $'
plt.plot(energy, refl_coat, label='Rh coated')
plt.plot(energy, refl_rhod, label='Rh bulk')
plt.title(title)
plt.xlabel('Energy (eV)')
plt.ylabel('Reflectivity')
plt.yscale('log')
plt.legend()
plt.show()
```

--------------------------------

### add_material(name, formula, density, categories=None)

Source: https://github.com/xraypy/xraydb/blob/master/doc/python.rst

Adds a new material to the user's local material database.

```APIDOC
## add_material(name, formula, density, categories=None)

### Description
Adds a custom material to the local configuration file for use in future sessions.

### Parameters
- **name** (str) - Required - Name of the material.
- **formula** (str) - Required - Chemical formula.
- **density** (float) - Required - Density of the material.
- **categories** (list of strings) - Optional - List of category names.

### Returns
- **None**
```

--------------------------------

### get_material(name)

Source: https://github.com/xraypy/xraydb/blob/master/doc/python.rst

Looks up a material by name and returns its formula and density.

```APIDOC
## get_material(name)

### Description
Retrieves the chemical formula and density for a specified material name.

### Parameters
- **name** (str) - Required - The name of the material or chemical formula.

### Returns
- **tuple** - A tuple containing the chemical formula (str) and density (float).
```

--------------------------------

### Calculate and plot Darwin widths

Source: https://github.com/xraypy/xraydb/blob/master/doc/examples.rst

Calculates Darwin widths for Si(111) and Si(333) crystals and plots their reflectivity profiles.

```python
import numpy as np
from xraydb import darwin_width
import matplotlib.pyplot as plt

dw_si111 = darwin_width(10000, 'Si', (1, 1, 1))
dw_si333 = darwin_width(30000, 'Si', (3, 3, 3))

print(dw_si111.theta_width*1e6)

fmt_string = "Darwin Width for {:s} at {:.0f} keV: {:5.2f} microrad, {:5.2f} eV"
print(fmt_string.format('Si(111)', 10,
                        dw_si111.theta_width*1e6,
                        dw_si111.energy_width))


print(fmt_string.format('Si(333)', 30,
                        dw_si333.theta_width*1e6,
                        dw_si333.energy_width))

dtheta  = dw_si111.dtheta*1e6
denergy = dw_si111.denergy[::-1]

#  slightly advanced matplotlib hackery:
fig, ax = plt.subplots(constrained_layout=True)


ax.plot(dtheta, dw_si111.intensity, label='$I$, Si(111)', linewidth=2)
ax.plot(dtheta, dw_si111.intensity**2, label='$I^2$, Si(111)', linewidth=2)
ax.plot(dw_si333.dtheta*1e6, dw_si333.intensity**2, label='$I^2$ Si(333) 30 keV', linewidth=2)


ax.set_title('X-ray diffraction intensity at 10keV')
ax.set_xlabel('Angle - $\theta_B$ ($ \mu \mathrm{rad}$)')
ax.set_ylabel('Reflectivity')
ax.legend()

plt.show()
```

```text
Darwin Width for Si(111) at 10 keV: 26.96 microrad,  1.34 eV
Darwin Width for Si(333) at 30 keV:  1.81 microrad,  0.27 eV
```

--------------------------------

### Calculate multilayer mirror reflectivity

Source: https://github.com/xraypy/xraydb/blob/master/doc/examples.rst

Uses multilayer_reflectivity to compute reflectivity for periodic layered structures on a substrate.

```python
import numpy as np
from xraydb import multilayer_reflectivity
import matplotlib.pyplot as plt

# 40 layers of [27Ang Si, 18Ang W]
materials = ['Si', 'W']
thicknesses = [27, 18] # angstroms
n_periods = 40
substrate = 'SiO2'
theta = 0.01
energy = np.linspace(500, 20000, 5000)

reflect = multilayer_reflectivity(materials, thicknesses, substrate,
                                  theta, energy, n_periods=n_periods)

plt.plot(energy, reflect)
plt.title(f'$\rm 40 x [27\AA\, Si,\, 18\AA\, W] \> multilayer \> \theta\, = \, {theta*1000:.0f}\> mrad$')
plt.xlabel('Energy (eV)')
plt.ylabel('Reflectivity')
plt.show()
```

--------------------------------

### material_mu_components(name, energy, density=None, kind='total')

Source: https://github.com/xraypy/xraydb/blob/master/doc/python.rst

Calculates the absorption coefficient (in 1/cm) for a compound and returns component details.

```APIDOC
## material_mu_components(name, energy, density=None, kind='total')

### Description
Calculates the absorption coefficient (in 1/cm) for a compound and returns a dictionary containing mass, density, elements, and per-element mu values.

### Parameters
- **name** (str) - Required - Chemical formula or name of material from materials list.
- **energy** (float or ndarray) - Required - Energy or array of energies in eV.
- **density** (None or float) - Optional - Material density (gr/cm^3).
- **kind** (str) - Optional - 'photo' or 'total' for whether to return the photo-absorption or total cross-section (default: 'total').

### Returns
- components (dict) - Dictionary with 'mass', 'density', 'elements' (list), and per-element tuples of (stoichiometric fraction, atomic mass, mu).
```

--------------------------------

### Add custom material

Source: https://github.com/xraypy/xraydb/blob/master/doc/python.rst

Adds a new material to the local user database, which persists across sessions.

```pycon
>>> xraydb.add_material('becopper', 'Cu0.98e0.02', 8.3, categories=['metal'])
```

--------------------------------

### f0_ions(element=None)

Source: https://github.com/xraypy/xraydb/blob/master/doc/python.rst

Lists ion names supported in the f0() calculation.

```APIDOC
## f0_ions(element=None)

### Description
Returns a list of strings for matching ion names supported in the f0() calculation.

### Parameters
- **element** (None, int, str) - Optional - Scatterer identifier.
```

--------------------------------

### mirror_reflectivity(formula, theta, energy, density=None, roughness=0.0, polarization='s', output='intensity')

Source: https://github.com/xraypy/xraydb/blob/master/doc/python.rst

Calculates the mirror reflectivity for a thick, single-layer mirror.

```APIDOC
## mirror_reflectivity

### Description
Calculates mirror reflectivity for a thick, single-layer mirror given material properties and geometry.

### Parameters
- **formula** (string) - Required - Material name or formula
- **theta** (float or nd-array) - Required - Mirror angle in radians
- **energy** (float or nd-array) - Required - X-ray energy in eV
- **density** (float or None) - Optional - Material density in g/cm^3
- **roughness** (float) - Optional - Mirror roughness in Angstroms. Default: 0.0
- **polarization** (string) - Optional - Mirror orientation ('s' or 'p'). Default: 's'
- **output** (string) - Optional - Output type ('intensity' or 'amplitude'). Default: 'intensity'

### Returns
- **reflectivity** (float or nd-array) - Mirror reflectivity values.
```

--------------------------------

### get_xraydb()

Source: https://github.com/xraypy/xraydb/blob/master/doc/python.rst

Returns an instance of the XrayDB object to access the database.

```APIDOC
## get_xraydb()

### Description
Returns an instance of the XrayDB object.

### Returns
- **XrayDB** - An instance of the XrayDB class.

### Example
```python
import xraydb
xdb = xraydb.get_xraydb()
```
```

--------------------------------

### xray_lines(element, initial_level=None, excitation_energy=None)

Source: https://github.com/xraypy/xraydb/blob/master/doc/python.rst

Retrieves a dictionary of X-ray emission lines for a given element. Excitation energy, if provided, supersedes the initial level parameter.

```APIDOC
## xray_lines(element, initial_level=None, excitation_energy=None)

### Description
Retrieves a dictionary of X-ray emission lines for a specified element. The returned dictionary uses Siegbahn notation as keys and XrayLine tuples as values.

### Parameters
- **element** (int, str) - Required - Atomic number or atomic symbol for the element.
- **initial_level** (None, str) - Optional - IUPAC symbol of the initial level.
- **excitation_energy** (None, float) - Optional - Excitation energy; if provided, it supersedes the initial_level parameter.

### Returns
- **dict** - Dictionary of X-ray lines containing (energy, intensity, initial level, final level) tuples.
```

--------------------------------

### Calculate material attenuation and components

Source: https://github.com/xraypy/xraydb/blob/master/doc/python.rst

Retrieves the attenuation coefficient and a dictionary of elemental components for a given material.

```pycon
>>> xraydb.material_mu('quartz', 10000)
50.36774553547068
>>> xraydb.material_mu_components('quartz', 10000)
{'mass': 60.0843, 'density': 2.65, 'elements': ['Si', 'O'],
'Si': (1, 28.0855, 33.87943243018506), 'O': (2.0, 15.9994, 5.952824815297084)}
```

--------------------------------

### Calculate 1/e absorption depth

Source: https://github.com/xraypy/xraydb/blob/master/doc/examples.rst

Calculates the 1/e absorption depth for a specific material at a given energy.

```python
>>> from xraydb import material_mu
>>> mu_20kev = xraydb.material_mu('CaCO3', 20000, density=2.71)
>>> print("CaCO3 1/e depth at 20keV = {:.3f} mm".format(10/mu_20kev))
CaCO3 1/e depth at 20keV = 0.648 mm
```

--------------------------------

### Retrieve X-ray emission lines for an element

Source: https://github.com/xraypy/xraydb/blob/master/doc/python.rst

Iterate through and print X-ray emission lines for a specific element and initial level.

```pycon
>>> for name, line in xraydb.xray_lines('Mn', 'K').items():
...     print(name, line)
...
Ka3 XrayLine(energy=5769.9, intensity=0.000265963, initial_level='K', final_level='L1')
Ka2 XrayLine(energy=5889.1, intensity=0.293941, initial_level='K', final_level='L2')
Ka1 XrayLine(energy=5900.3, intensity=0.58134, initial_level='K', final_level='L3')
Kb3 XrayLine(energy=6491.8, intensity=0.042234, initial_level='K', final_level='M2')
Kb1 XrayLine(energy=6491.8, intensity=0.0815329, initial_level='K', final_level='M3')
Kb5 XrayLine(energy=6537.0, intensity=0.000685981, initial_level='K', final_level='M4,5')
```

--------------------------------

### Calculate single layer mirror reflectivity

Source: https://github.com/xraypy/xraydb/blob/master/doc/examples.rst

Uses mirror_reflectivity to compare energy-dependent reflectivity across different materials at a fixed incident angle.

```python
import numpy as np
from xraydb import mirror_reflectivity
import matplotlib.pyplot as plt

energy = np.linspace(1000, 51000, 501)

r_si = mirror_reflectivity('Si', 0.002, energy)
r_ni = mirror_reflectivity('Ni', 0.002, energy)
r_rh = mirror_reflectivity('Rh', 0.002, energy)
r_pt = mirror_reflectivity('Pt', 0.002, energy)

plt.plot(energy, r_si, label='Si')
plt.plot(energy, r_ni, label='Ni')
plt.plot(energy, r_rh, label='Rh')
plt.plot(energy, r_pt, label='Pt')

plt.title('X-ray reflectivity at $\theta=2 \mathrm{mrad}$')
plt.xlabel('Energy (eV)')
plt.ylabel('Reflectivity')
plt.legend()
plt.show()
```

--------------------------------

### find_material(name)

Source: https://github.com/xraypy/xraydb/blob/master/doc/python.rst

Looks up a material by name or formula and returns its instance.

```APIDOC
## find_material(name)

### Description
Retrieves a material instance based on its name or chemical formula.

### Parameters
- **name** (str) - Required - The name of the material or chemical formula.

### Returns
- **Material** - The material instance.
```

--------------------------------

### darwin_width(energy, crystal='Si', hkl=(1, 1, 1), a=None, polarization='s', ignore_f2=False, ignore_f1=False, m=1)

Source: https://github.com/xraypy/xraydb/blob/master/doc/python.rst

Calculates the Darwin width for a specific crystal reflection and X-ray energy.

```APIDOC
## darwin_width

### Description
Calculates the Darwin width for a crystal reflection and energy. Returns a named tuple 'DarwinWidth' containing various angular and energy width parameters.

### Parameters
- **energy** (float) - Required - X-ray energy in eV
- **crystal** (string) - Optional - Name of crystal ('Si', 'Ge', or 'C'). Default: 'Si'
- **hkl** (tuple) - Optional - h, k, l for reflection. Default: (1, 1, 1)
- **a** (float or None) - Optional - Lattice constant. Default: None
- **polarization** (string) - Optional - Mono orientation ('s', 'p', 'u'). Default: 's'
- **ignore_f1** (bool) - Optional - Ignore contribution from f1. Default: False
- **ignore_f2** (bool) - Optional - Ignore contribution from f2. Default: False
- **m** (int) - Optional - Order of reflection. Default: 1

### Returns
- **DarwinWidth** (named tuple) - Contains fields: theta, theta_offset, theta_width, theta_fwhm, rocking_theta_fwhm, energy_width, energy_fwhm, rocking_energy_fwhm, zeta, dtheta, denergy, intensity, rocking_curve.
```

--------------------------------

### Calculate fluorescence yield

Source: https://github.com/xraypy/xraydb/blob/master/doc/python.rst

Calculate fluorescence yield, average energy, and net probability for specific elements and X-ray lines.

```pycon
>>> xraydb.fluor_yield('Fe', 'K', 'Ka', 8000)
0.350985, 6400.752419799043, 0.874576096
```

```pycon
>>> xraydb.fluor_yield('Fe', 'K', 'Ka', 6800)
0.0, 6400.752419799043, 0.874576096
```

```pycon
>>> xraydb.fluor_yield('Ag', 'L3', 'La', 6000)
0.052, 2982.129655446868, 0.861899000000000
```

--------------------------------

### ionchamber_fluxes(gas='nitrogen', volts=1.0, length=100.0, energy=10000.0, sensitivity=1e-06, sensitivity_units='A/V', with_compton=True, both_carriers=True)

Source: https://github.com/xraypy/xraydb/blob/master/doc/python.rst

Calculates ion chamber and PIN diode fluxes for a gas, mixture of gases, or semiconductor material.

```APIDOC
## ionchamber_fluxes

### Description
Calculates incident, transmitted, and absorbed X-ray fluxes for an ion chamber or PIN diode. It accounts for gas composition, chamber length, X-ray energy, and current amplifier settings.

### Parameters
- **gas** (string or dict) - Optional - Name or formula of fill gas or diode material, or a dictionary of gas fractions. Default: 'nitrogen'.
- **volts** (float) - Optional - Measured voltage output of current amplifier. Default: 1.0.
- **length** (float) - Optional - Active length of ion chamber in cm. Default: 100.0.
- **energy** (float) - Optional - X-ray energy in eV. Default: 10000.0.
- **sensitivity** (float) - Optional - Current amplifier sensitivity. Default: 1e-06.
- **sensitivity_units** (string) - Optional - Units of current amplifier sensitivity. Default: 'A/V'.
- **with_compton** (bool) - Optional - Switch to control the contribution of Compton scattering. Default: True.
- **both_carriers** (bool) - Optional - Switch to control whether to count both electron and ion current. Default: True.

### Returns
- **IonchamberFluxes** (named tuple) - Contains fields: incident (Hz), transmitted (Hz), photo (Hz), and incoherent (Hz).
```

--------------------------------

### Atomic and Material Functions

Source: https://github.com/xraypy/xraydb/blob/master/doc/python.rst

A collection of functions for calculating atomic properties, cross-sections, and material characteristics.

```APIDOC
## Atomic and Material Functions

- **ck_probability()**: Coster-Kronig transition probability between two atomic levels.
- **mu_elam()**: Absorption cross-section, photo-electric or total for an element.
- **coherent_cross_section_elam()**: Coherent scattering cross-section for an element.
- **incoherent_cross_section_elam()**: Incoherent scattering cross-section for an element.
- **chantler_energies()**: Energies of tabulation for Chantler data.
- **f1_chantler()**: f'(E) anomalous scattering factor.
- **f2_chantler()**: f"(E) anomalous scattering factor.
- **mu_chantler()**: Absorption cross-section.
- **guess_edge()**: Guess element and edge from energy of absorption edge.
- **chemparse()**: Parse a chemical formula to atomic abundances.
- **validate_formula()**: Test whether a chemical formula can be parsed.
- **get_materials()**: Get a dictionary of known materials {name:(formula, density)}.
- **get_material()**: Get a (formula, density) tuple for a material in the materials database.
- **find_material()**: Get a material instance for a material in the materials database.
- **add_material()**: Add a material to local materials database.
- **material_mu()**: Absorption cross-section for a material at X-ray energies.
- **material_mu_components()**: Dictionary of elemental components of mu for material.
- **xray_delta_beta()**: Anomalous index of refraction for material and energy.
- **darwin_width()**: Darwin widths for monochromator crystals.
- **mirror_reflectivity()**: X-ray reflectivities for mirror materials (thick slab limit).
- **multilayer_reflectivity()**: X-ray reflectivities for multilayer mirrors.
- **coated_reflectivity()**: X-ray reflectivities for coated mirrors.
- **ionization_potential()**: Effective ionization potential for a gas, as for ion chambers.
- **ionchamber_fluxes()**: Calculate fluxes from ion chamber voltages, gases, and sensitivities.
```

--------------------------------

### f0(ion, q)

Source: https://github.com/xraypy/xraydb/blob/master/doc/python.rst

Calculates the elastic X-ray scattering factor, f0(q), for an ion.

```APIDOC
## f0(ion, q)

### Description
Calculates the elastic X-ray scattering factor, f0(q), for an ion.

### Parameters
- **ion** (int, str) - Required - Atomic number, atomic symbol, or ionic symbol.
- **q** (float, ndarray) - Required - Q value(s) for scattering.
```

--------------------------------

### material_mu(name, energy, density=None, kind='total')

Source: https://github.com/xraypy/xraydb/blob/master/doc/python.rst

Calculates the X-ray attenuation length (in 1/cm) for a material by name or formula.

```APIDOC
## material_mu(name, energy, density=None, kind='total')

### Description
Calculates the X-ray attenuation length (in 1/cm) for a material by name or formula.

### Parameters
- **name** (str) - Required - Chemical formula or name of material from materials list.
- **energy** (float or ndarray) - Required - Energy or array of energies in eV.
- **density** (None or float) - Optional - Material density (gr/cm^3).
- **kind** (str) - Optional - 'photo' or 'total' for whether to return the photo-absorption or total cross-section (default: 'total').

### Returns
- absorption length (float) - The absorption length in 1/cm.
```

--------------------------------

### xray_delta_beta(material, density, energy)

Source: https://github.com/xraypy/xraydb/blob/master/doc/python.rst

Calculates the anomalous components of the index of refraction for a material.

```APIDOC
## xray_delta_beta(material, density, energy)

### Description
Calculates the anomalous components of the index of refraction for a material using tabulated scattering components.

### Parameters
- **material** (str) - Required - Chemical formula (e.g., 'Fe2O3').
- **density** (float) - Required - Material density in g/cm^3.
- **energy** (float) - Required - X-ray energy in eV.

### Returns
- (delta, beta, atlen) (tuple) - Returns the real part of index of refraction (delta), imaginary part (beta), and attenuation length (atlen) in cm.
```

--------------------------------

### Define TikZ Styles for X-ray Diagrams

Source: https://github.com/xraypy/xraydb/blob/master/poster/elines.tex

These styles configure line properties, fonts, and positioning for energy levels and transition paths.

```latex
glevel/.style=line width=0.8mm, draw=black!40
blevel/.style=line width=0.8mm, draw=blue!80
rlevel/.style=line width=0.8mm, draw=red!80
xray/.style=*->,>=triangle 45, line width=1mm, font=
sieg/.style=fill=white, font=
frac/.style=above,fill=white
edge/.style=left, font=
orbital/.style=right, font=
xjoin/.style=*-, line width=1mm
```

--------------------------------

### Calculate Ion Chamber Fluxes for Gas Mixtures

Source: https://github.com/xraypy/xraydb/blob/master/doc/python.rst

Computes flux values for a mixture of gases by passing a dictionary defining the relative fractions.

```pycon
>>> fl = ionchamber_fluxes(gas={'nitrogen':0.5, 'helium': 0.5},
                           volts=1.25, length=20.0, energy=10000.0,
                           sensitivity=1.e-6)
```

```pycon
>>> print(f"Fluxes: In={fl.incident:g}, Out={fl.transmitted:g}, Transmitted={100*fl.transmitted/fl.incident:.2f}%")
Fluxes: In=6.83845e+11, Out=6.51188e+11, Transmitted=95.22%
```

--------------------------------

### guess_edge(energy, edges=('K', 'L3', 'L2', 'L1', 'M5'))

Source: https://github.com/xraypy/xraydb/blob/master/doc/python.rst

Estimates an element and edge based on a provided energy value.

```APIDOC
## guess_edge(energy, edges=('K', 'L3', 'L2', 'L1', 'M5'))

### Description
Guesses the most likely element and edge based on an approximate energy value in eV.

### Parameters
- **energy** (float) - Required - The approximate edge energy in eV.
- **edges** (list of strings) - Optional - The list of edges to consider. Defaults to ('K', 'L3', 'L2', 'L1', 'M5').

### Returns
- **tuple** - A tuple containing (atomic symbol, edge) for the best guess.
```

--------------------------------

### Plot X-ray mass attenuation for selected elements

Source: https://github.com/xraypy/xraydb/blob/master/doc/examples.rst

Calculates and plots the total mass attenuation coefficient for Carbon, Copper, and Gold across a range of energies using mu_elam.

```python
#!/usr/bin/env python
# XrayDB example script python/examples/mu_elements.py
#
# plot X-ray mass attenuation for selected elements
#
import numpy as np
import matplotlib.pyplot as plt
import wxmplot.interactive as wi
from xraydb import mu_elam , atomic_symbol

energy = np.arange(500, 120000, 10)  # energy in eV
      
for elem in ('C', 'Cu', 'Au'):
    mu = mu_elam(elem, energy)
    plt.plot(energy, mu, label=elem, linewidth=2)
 
plt.title('X-ray mass attenuation')
plt.xlabel('Energy (eV)')
plt.ylabel(r'$\mu/\rho \rm\, (cm^2/gr)$')
plt.legend()
plt.yscale('log')
plt.xscale('log')
plt.show()
```

--------------------------------

### Plot X-ray rocking curve

Source: https://github.com/xraypy/xraydb/blob/master/doc/examples.rst

Visualizes the intensity of a single reflection compared to the rocking curve of two crystals.

```python
import numpy as np
from xraydb import darwin_width
import matplotlib.pyplot as plt

dw_si111 = darwin_width(10000, 'Si', (1, 1, 1))

dtheta  = dw_si111.dtheta*1e6

fig, ax = plt.subplots(constrained_layout=True)

ax.plot(dtheta, dw_si111.intensity, label='$I$, 1 crystal', linewidth=2)
ax.plot(dtheta, dw_si111.rocking_curve, label='Rocking Curve', linewidth=2)


ax.set_title('X-ray Rocking Curve at 10keV, Si(111)')
ax.set_xlabel('Angle - $\theta_B$ ($ \mu 	ext{rad}$)')
ax.set_ylabel('Reflectivity')
ax.legend()

plt.show()
```

--------------------------------

### atomic_density(element)

Source: https://github.com/xraypy/xraydb/blob/master/doc/python.rst

Retrieves the density (gr/cm^3) for the common form of an element.

```APIDOC
## atomic_density(element)

### Description
Returns the density (gr/cm^3) for the common form of an element.

### Parameters
- **element** (int, str) - Required - Atomic number or atomic symbol.
```

--------------------------------

### Calculate Darwin Width

Source: https://github.com/xraypy/xraydb/blob/master/doc/python.rst

Computes the Darwin width for a specified crystal reflection and X-ray energy. Requires the crystal structure to be one of Si, Ge, or C.

```python
>>> dw = darwin_width(10000, crystal=’Si’, hkl=(1, 1, 1))
>>> print(dw.theta_width, dw.energy_width)
2.695922108316184e-05 1.336668903324966
```

--------------------------------

### mu_elam(element, energy, kind='total')

Source: https://github.com/xraypy/xraydb/blob/master/doc/python.rst

Retrieves the X-ray mass attenuation coefficient (mu/rho) for a given element and energy using Elam tables.

```APIDOC
## mu_elam(element, energy, kind='total')

### Description
Returns the X-ray mass attenuation coefficient (mu/rho) for an element and energy or array of energies. Data is sourced from the Elam tables.

### Parameters
- **element** (int, str) - Required - Atomic number or atomic symbol for the element.
- **energy** (float, ndarray) - Required - Energy or array of energies.
- **kind** (str) - Optional - Type of cross-section to use: 'total', 'photo', 'coh', or 'incoh'. Defaults to 'total'.

### Returns
- float or ndarray - The attenuation coefficient in cm^2/gr.
```
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