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Merged
jacklovell merged 2 commits into from
Jul 31, 2024
Merged

Improve and expand the documentation for the atomic data repository #453

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8934c8c
Improve documentation for openadas repository install and manipulatio…
vsnever Jul 24, 2024
db0f614
Merge branch 'development' into docs/atomic_repository_manipulation
vsnever Jul 31, 2024
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61 changes: 35 additions & 26 deletions cherab/openadas/install.py
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Original file line number Diff line number Diff line change
Expand Up @@ -269,14 +269,17 @@ def install_adf15(element, ionisation, file_path, download=False, repository_pat


def install_adf21(beam_species, target_ion, target_charge, file_path, download=False, repository_path=None, adas_path=None):
# """
# Adds the rate defined in an ADF21 file to the repository.
#
# :param file_path: Path relative to ADAS root.
# :param download: Attempt to download file if not present (Default=True).
# :param repository_path: Path to the repository in which to install the rates (optional).
# :param adas_path: Path to ADAS files repository (optional).
# """
"""
Adds the beam stopping rate defined in an ADF21 file to the repository.

:param beam_species: Beam neutral atom (Element/Isotope).
:param target_ion: Target species (Element/Isotope).
:param target_charge: Charge of the target species.
:param file_path: Path relative to ADAS root.
:param download: Attempt to download file if not present (Default=True).
:param repository_path: Path to the repository in which to install the rates (optional).
:param adas_path: Path to ADAS files repository (optional).
"""

print('Installing {}...'.format(file_path))
path = _locate_adas_file(file_path, download, adas_path, repository_path)
Expand All @@ -289,15 +292,18 @@ def install_adf21(beam_species, target_ion, target_charge, file_path, download=F


def install_adf22bmp(beam_species, beam_metastable, target_ion, target_charge, file_path, download=False, repository_path=None, adas_path=None):
pass
# """
# Adds the rate defined in an ADF21 file to the repository.
#
# :param file_path: Path relative to ADAS root.
# :param download: Attempt to download file if not present (Default=True).
# :param repository_path: Path to the repository in which to install the rates (optional).
# :param adas_path: Path to ADAS files repository (optional).
# """
"""
Adds the beam population rate defined in an ADF22 BMP file to the repository.

:param beam_species: Beam neutral atom (Element/Isotope).
:param beam_metastable: Metastable/excitation level of beam neutral atom.
:param target_ion: Target species (Element/Isotope).
:param target_charge: Charge of the target species.
:param file_path: Path relative to ADAS root.
:param download: Attempt to download file if not present (Default=True).
:param repository_path: Path to the repository in which to install the rates (optional).
:param adas_path: Path to ADAS files repository (optional).
"""

print('Installing {}...'.format(file_path))
path = _locate_adas_file(file_path, download, adas_path, repository_path)
Expand All @@ -310,15 +316,18 @@ def install_adf22bmp(beam_species, beam_metastable, target_ion, target_charge, f


def install_adf22bme(beam_species, target_ion, target_charge, transition, file_path, download=False, repository_path=None, adas_path=None):
pass
# """
# Adds the rate defined in an ADF21 file to the repository.
#
# :param file_path: Path relative to ADAS root.
# :param download: Attempt to download file if not present (Default=True).
# :param repository_path: Path to the repository in which to install the rates (optional).
# :param adas_path: Path to ADAS files repository (optional).
# """
"""
Adds the beam emission rate defined in an ADF22 BME file to the repository.

:param beam_species: Beam neutral atom (Element/Isotope).
:param target_ion: Target species (Element/Isotope).
:param target_charge: Charge of the target species.
:param transition: Tuple containing (initial level, final level).
:param file_path: Path relative to ADAS root.
:param download: Attempt to download file if not present (Default=True).
:param repository_path: Path to the repository in which to install the rates (optional).
:param adas_path: Path to ADAS files repository (optional).
"""

print('Installing {}...'.format(file_path))
path = _locate_adas_file(file_path, download, adas_path, repository_path)
Expand Down
143 changes: 121 additions & 22 deletions cherab/openadas/repository/atomic.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
# Copyright 2016-2018 Euratom
# Copyright 2016-2018 United Kingdom Atomic Energy Authority
# Copyright 2016-2018 Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas
# Copyright 2016-2024 Euratom
# Copyright 2016-2024 United Kingdom Atomic Energy Authority
# Copyright 2016-2024 Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas
#
# Licensed under the EUPL, Version 1.1 or – as soon they will be approved by the
# European Commission - subsequent versions of the EUPL (the "Licence");
Expand Down Expand Up @@ -34,8 +34,15 @@ def add_ionisation_rate(species, charge, rate, repository_path=None):
function instead. The update function avoids repeatedly opening and closing
the rate files.

:param repository_path:
:return:
:param species: Plasma species (Element/Isotope).
:param charge: Charge of the plasma species.
:param rate: Ionisation rate dictionary containing the following entries:

| 'ne': array-like of size (N) with electron density in m^-3,
| 'te': array-like of size (M) with electron temperature in eV,
| 'rate': array-like of size (N, M) with ionisation rate in m^3.s^-1.

:param repository_path: Path to the atomic data repository.
"""

update_ionisation_rates({
Expand All @@ -47,11 +54,21 @@ def add_ionisation_rate(species, charge, rate, repository_path=None):

def update_ionisation_rates(rates, repository_path=None):
"""
Ionisation rate file structure

/ionisation/<species>.json
Updates the ionisation rate files `/ionisation/<species>.json`
in atomic data repository.

File contains multiple rates, indexed by the ion charge state.

:param rates: Dictionary in the form {<species>: {<charge>: <rate>}}, where

| <species> is the plasma species (Element/Isotope),
| <charge> is the charge of the plasma species,
| <rate> is the ionisation rate dictionary containing the following entries:
| 'ne': array-like of size (N) with electron density in m^-3,
| 'te': array-like of size (M) with electron temperature in eV,
| 'rate': array-like of size (N, M) with ionisation rate in m^3.s^-1.

:param repository_path: Path to the atomic data repository.
"""

repository_path = repository_path or DEFAULT_REPOSITORY_PATH
Expand All @@ -75,8 +92,15 @@ def add_recombination_rate(species, charge, rate, repository_path=None):
function instead. The update function avoids repeatedly opening and closing
the rate files.

:param repository_path:
:return:
:param species: Plasma species (Element/Isotope).
:param charge: Charge of the plasma species.
:param rate: Recombination rate dictionary containing the following entries:

| 'ne': array-like of size (N) with electron density in m^-3,
| 'te': array-like of size (M) with electron temperature in eV,
| 'rate': array-like of size (N, M) with recombination rate in m^3.s^-1.

:param repository_path: Path to the atomic data repository.
"""

update_recombination_rates({
Expand All @@ -88,11 +112,21 @@ def add_recombination_rate(species, charge, rate, repository_path=None):

def update_recombination_rates(rates, repository_path=None):
"""
Ionisation rate file structure

/recombination/<species>.json
Updates the recombination rate files `/recombination/<species>.json`
in the atomic data repository.

File contains multiple rates, indexed by the ion charge state.

:param rates: Dictionary in the form {<species>: {<charge>: <rate>}}, where

| <species> is the plasma species (Element/Isotope),
| <charge> is the charge of the plasma species,
| <rate> is the recombination rate dictionary containing the following entries:
| 'ne': array-like of size (N) with electron density in m^-3,
| 'te': array-like of size (M) with electron temperature in eV,
| 'rate': array-like of size (N, M) with recombination rate in m^3.s^-1.

:param repository_path: Path to the atomic data repository.
"""

repository_path = repository_path or DEFAULT_REPOSITORY_PATH
Expand All @@ -109,7 +143,6 @@ def update_recombination_rates(rates, repository_path=None):


def add_thermal_cx_rate(donor_element, donor_charge, receiver_element, rate, repository_path=None):

"""
Adds a single thermal charge exchange rate to the repository.

Expand All @@ -118,11 +151,16 @@ def add_thermal_cx_rate(donor_element, donor_charge, receiver_element, rate, rep
the rate files.

:param donor_element: Element donating the electron.
:param donor_charge: Charge of the donating atom/ion
:param receiver_element: Element receiving the electron
:param rate: rates
:param repository_path:
:return:
:param donor_charge: Charge of the donating atom/ion.
:param receiver_element: Element receiving the electron.
:param receiver_charge: Charge of the receiving atom/ion.
:param rate: Thermal CX rate dictionary containing the following entries:

| 'ne': array-like of size (N) with electron density in m^-3,
| 'te': array-like of size (M) with electron temperature in eV,
| 'rate': array-like of size (N, M) with thermal CX rate in m^3.s^-1.

:param repository_path: Path to the atomic data repository.
"""

rates2update = RecursiveDict()
Expand All @@ -133,11 +171,25 @@ def add_thermal_cx_rate(donor_element, donor_charge, receiver_element, rate, rep

def update_thermal_cx_rates(rates, repository_path=None):
"""
Thermal charge exchange rate file structure

/thermal_cx/<donor_element>/<donor_charge>/<receiver_element>.json
Updates the thermal charge exchange rate files
`/thermal_cx/<donor_element>/<donor_charge>/<receiver_element>.json`
in the atomic data repository.

File contains multiple rates, indexed by the ion charge state.

:param rates: Dictionary in the form:

| { <donor_element>: { <donor_charge>: { <receiver_element>: { <donor_charge>: <rate> } } } }, where
| <donor_element> is the element donating the electron.
| <donor_charge> is the charge of the donating atom/ion.
| <receiver_element> is the element receiving the electron.
| <receiver_charge> is the charge of the receiving atom/ion.
| <rate> is the thermal CX rate dictionary containing the following entries:
| 'ne': array-like of size (N) with electron density in m^-3,
| 'te': array-like of size (M) with electron temperature in eV,
| 'rate': array-like of size (N, M) with thermal CX rate in m^3.s^-1.

:param repository_path: Path to the atomic data repository.
"""

repository_path = repository_path or DEFAULT_REPOSITORY_PATH
Expand Down Expand Up @@ -203,6 +255,21 @@ def _update_and_write_adf11(species, rate_data, path):


def get_ionisation_rate(element, charge, repository_path=None):
"""
Reads the ionisation rate for the given species and charge
from the atomic data repository.

:param element: Plasma species (Element/Isotope).
:param charge: Charge of the plasma species.
:param repository_path: Path to the atomic data repository.

:return rate: Ionisation rate dictionary containing the following entries:

| 'ne': 1D array of size (N) with electron density in m^-3,
| 'te': 1D array of size (M) with electron temperature in eV,
| 'rate': 2D array of size (N, M) with ionisation rate in m^3.s^-1.

"""

repository_path = repository_path or DEFAULT_REPOSITORY_PATH

Expand All @@ -224,6 +291,21 @@ def get_ionisation_rate(element, charge, repository_path=None):


def get_recombination_rate(element, charge, repository_path=None):
"""
Reads the recombination rate for the given species and charge
from the atomic data repository.

:param element: Plasma species (Element/Isotope).
:param charge: Charge of the plasma species.
:param repository_path: Path to the atomic data repository.

:return rate: Recombination rate dictionary containing the following entries:

| 'ne': 1D array of size (N) with electron density in m^-3,
| 'te': 1D array of size (M) with electron temperature in eV,
| 'rate': 2D array of size (N, M) with recombination rate in m^3.s^-1.

"""

repository_path = repository_path or DEFAULT_REPOSITORY_PATH

Expand All @@ -245,6 +327,23 @@ def get_recombination_rate(element, charge, repository_path=None):


def get_thermal_cx_rate(donor_element, donor_charge, receiver_element, receiver_charge, repository_path=None):
"""
Reads the thermal charge exchange rate for the given species and charge
from the atomic data repository.

:param donor_element: Element donating the electron.
:param donor_charge: Charge of the donating atom/ion.
:param receiver_element: Element receiving the electron.
:param receiver_charge: Charge of the receiving atom/ion.
:param repository_path: Path to the atomic data repository.

:return rate: Thermal CX rate dictionary containing the following entries:

| 'ne': 1D array of size (N) with electron density in m^-3,
| 'te': 1D array of size (M) with electron temperature in eV,
| 'rate': 2D array of size (N, M) with thermal CX rate in m^3.s^-1.

"""

repository_path = repository_path or DEFAULT_REPOSITORY_PATH

Expand Down
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