Update cherab-adas to support the new concept of atomic data repository

cherab/adas/__init__.py

@@ -1,6 +1,6 @@
-# Copyright 2016-2021 Euratom
-# Copyright 2016-2021 United Kingdom Atomic Energy Authority
-# Copyright 2016-2021 Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas
+# Copyright 2016-2023 Euratom
+# Copyright 2016-2023 United Kingdom Atomic Energy Authority
+# Copyright 2016-2023 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");
@@ -16,4 +16,6 @@
 # See the Licence for the specific language governing permissions and limitations
 # under the Licence.
 
-from .adas import ADAS
+from cherab.atomic.atomicdata import AtomicData as ADAS
+
+from . import install

cherab/adas/adas4xx/__init__.py

@@ -1,6 +1,6 @@
-# Copyright 2016-2021 Euratom
-# Copyright 2016-2021 United Kingdom Atomic Energy Authority
-# Copyright 2016-2021 Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas
+# Copyright 2016-2023 Euratom
+# Copyright 2016-2023 United Kingdom Atomic Energy Authority
+# Copyright 2016-2023 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");

cherab/adas/adas4xx/adas405.py

@@ -1,6 +1,6 @@
-# Copyright 2016-2021 Euratom
-# Copyright 2016-2021 United Kingdom Atomic Energy Authority
-# Copyright 2016-2021 Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas
+# Copyright 2016-2023 Euratom
+# Copyright 2016-2023 United Kingdom Atomic Energy Authority
+# Copyright 2016-2023 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");
@@ -29,6 +29,26 @@
 
 
 def run_adas405(uid='adas', year=96, elem='ne'):
+    """
+    Runs ADAS405 routine and gets radiated power for a given element.
+
+    :param uid: Username of adf11 location. Defaults to 'adas' for central ADAS data.
+    :param year: Year index of the adf11 data. Defaults to 96.
+    :param elem: Element symbol. Defaults to 'ne'.
+
+    :returns:
+
+    |    ne: electron density array of size N,
+    |    te: electron temperature array of size M,
+    |    fractional_abundance: (N, M, K) array with fractional abundances,
+    |    total_power: (N, M) array with total radiated power,
+    |    line_power: (N, M) array with line power driven by excitation of dominant ions,
+    |    continuum_power: (N, M) array with continuum and line power driven by recombination
+    |        and Bremsstrahlung of dominant ions,
+    |    cx_power: (N, M) array with line power due to charge transfer from thermal neutral
+    |        hydrogen to dominant ions,
+    |    stage_resolved_line_power: (N, M, K) array with line power resolved over ionisation stage.
+    """
 
     unique_cache_id = (uid, year, elem)
 

cherab/adas/adas6xx/__init__.py

@@ -1,6 +1,6 @@
-# Copyright 2016-2021 Euratom
-# Copyright 2016-2021 United Kingdom Atomic Energy Authority
-# Copyright 2016-2021 Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas
+# Copyright 2016-2023 Euratom
+# Copyright 2016-2023 United Kingdom Atomic Energy Authority
+# Copyright 2016-2023 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");
@@ -16,4 +16,4 @@
 # See the Licence for the specific language governing permissions and limitations
 # under the Licence.
 
-from .adas603 import run_adas603, print_adas603_supported_lines
+from .adas603 import run_adas603, print_adas603_supported_lines, SUPPORTED_LINES

cherab/adas/adas6xx/adas603.py

@@ -1,6 +1,6 @@
-# Copyright 2016-2021 Euratom
-# Copyright 2016-2021 United Kingdom Atomic Energy Authority
-# Copyright 2016-2021 Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas
+# Copyright 2016-2023 Euratom
+# Copyright 2016-2023 United Kingdom Atomic Energy Authority
+# Copyright 2016-2023 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");
@@ -105,6 +105,9 @@
 HDLIKE += [Line(neon, 9, (j, 13)) for j in range(15, 21)]
 
 
+SUPPORTED_LINES = MULTIPLETS + HDLIKE
+
+
 B_FIELD_MAX = {line: None for line in MULTIPLETS + HDLIKE}
 for isotope in (hydrogen, deuterium, tritium):
     for i in (1, 4):
@@ -208,9 +211,8 @@ def run_adas603(line, b_field=None, adas_fort=None):
     if not os.path.isfile(file_path):
         raise IOError('File {} not found.'.format(file_path))
 
-    pi_components = []
-    sigma_plus_components = []
-    sigma_minus_components = []
+    wavelength_list = []
+    ratio_list = []
 
     for b in b_field:
         process = Popen([file_path], stdin=PIPE, stdout=PIPE, stderr=PIPE)
@@ -222,41 +224,49 @@ def run_adas603(line, b_field=None, adas_fort=None):
         if errors:
             raise IOError('Process {} is terminated with error: {}.'.format(file_path, errors.decode('utf-8')))
 
-        pi_comp, sigma_plus_comp, sigma_minus_comp = _adas603_output_to_components(outs.decode('utf-8'))
+        polarisation, wavelength, ratio = _adas603_output_to_components(outs.decode('utf-8'))
 
-        pi_components.append(pi_comp)
-        sigma_plus_components.append(sigma_plus_comp)
-        sigma_minus_components.append(sigma_minus_comp)
+        wavelength_list.append(wavelength)
+        ratio_list.append(ratio)
 
-    return b_field, np.array(pi_components).T, np.array(sigma_plus_components).T, np.array(sigma_minus_components).T
+    data = {
+        'b': b_field,
+        'polarisation': polarisation,
+        'wavelength': np.array(wavelength_list).T,
+        'ratio': np.array(ratio_list).T,
+        'reference': 'ADAS {}'.format(executable)
+    }
+
+    return data
 
 
 def _adas603_output_to_components(outs):
     lines = outs.splitlines()
-    pi_components = []
-    sigma_plus_components = []
-    sigma_minus_components = []
+    ratio = []
+    wavelength = []
+    polarisation = []
     for line in lines:
         if '#' in line:
             columns = line.split('#')
             intensity = float(columns[-1])
-            wavelength = 0.1 * float(columns[-2])
-            polarisation = int(columns[-3].split('/')[0])
+            wvl = 0.1 * float(columns[-2])
+            pol = int(columns[-3].split('/')[0])
 
-            if polarisation == 0:  # pi components
-                pi_components.append([wavelength, intensity])
-            elif polarisation > 0:  # sigma+ components
-                sigma_plus_components.append([wavelength, intensity])
-            elif polarisation < 0:  # sigma- components
-                sigma_minus_components.append([wavelength, intensity])
+            polarisation.append(np.sign(pol))
+            wavelength.append(wvl)
+            ratio.append(intensity)
 
-    pi_components = np.array(pi_components).T
-    sigma_plus_components = np.array(sigma_plus_components).T
-    sigma_minus_components = np.array(sigma_minus_components).T
+    polarisation = np.array(polarisation, dtype=np.int32)
+    wavelength = np.array(wavelength)
+    ratio = np.array(ratio)
 
     # renormalising
-    pi_components[1] /= pi_components[1].sum()
-    sigma_plus_components[1] /= sigma_plus_components[1].sum()
-    sigma_minus_components[1] /= sigma_minus_components[1].sum()
+    index_pi, = np.where(polarisation == 0)
+    index_sigma_plus, = np.where(polarisation == 1)
+    index_sigma_minus, = np.where(polarisation == -1)
+
+    ratio[index_pi] /= ratio[index_pi].sum()
+    ratio[index_sigma_plus] /= ratio[index_sigma_plus].sum()
+    ratio[index_sigma_minus] /= ratio[index_sigma_minus].sum()
 
-    return pi_components, sigma_plus_components, sigma_minus_components
+    return polarisation, wavelength, ratio

cherab/adas/install.py

@@ -1,6 +1,6 @@
-# Copyright 2016-2021 Euratom
-# Copyright 2016-2021 United Kingdom Atomic Energy Authority
-# Copyright 2016-2021 Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas
+# Copyright 2016-2023 Euratom
+# Copyright 2016-2023 United Kingdom Atomic Energy Authority
+# Copyright 2016-2023 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");
@@ -19,12 +19,19 @@
 
 import os
 
-from cherab.adas import repository
+from cherab.atomic import repository
 from cherab.adas.parse import *
+from cherab.adas.adas6xx.adas603 import SUPPORTED_LINES as ADAS603_SUPPORTED_LINES
+from cherab.adas.adas6xx import run_adas603
+from cherab.adas.adas4xx import run_adas405
 from cherab.core.utility import RecursiveDict, PerCm3ToPerM3, Cm3ToM3
 
 
 def install_files(configuration, repository_path=None, adas_home=None):
+    """
+    Wrapper function that installs rates of atomic processes defined
+    in ADAS files to the repository.
+    """
 
     for adf in configuration:
         if adf.lower() == 'adf11scd':
@@ -255,13 +262,17 @@ def install_adf15(element, ionisation, file_path, repository_path=None, adas_hom
 
 
 def install_adf21(beam_species, target_ion, target_charge, file_path, repository_path=None, adas_home=None):
-    # """
-    # Adds the rate defined in an ADF21 file to the repository.
-    #
-    # :param file_path: Path relative to ADAS home.
-    # :param repository_path: Path to the repository in which to install the rates (optional).
-    # :param adas_home: Path to ADAS home directory (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_home: Path to ADAS home directory (optional).
+    """
 
     print('Installing {}...'.format(file_path))
     path = _locate_adas_file(file_path, adas_home)
@@ -274,14 +285,18 @@ def install_adf21(beam_species, target_ion, target_charge, file_path, repository
 
 
 def install_adf22bmp(beam_species, beam_metastable, target_ion, target_charge, file_path, repository_path=None, adas_home=None):
-    pass
-    # """
-    # Adds the rate defined in an ADF21 file to the repository.
-    #
-    # :param file_path: Path relative to ADAS home.
-    # :param repository_path: Path to the repository in which to install the rates (optional).
-    # :param adas_home: Path to ADAS home directory (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 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_home: Path to ADAS home directory (optional).
+    """
 
     print('Installing {}...'.format(file_path))
     path = _locate_adas_file(file_path, adas_home)
@@ -294,14 +309,18 @@ def install_adf22bmp(beam_species, beam_metastable, target_ion, target_charge, f
 
 
 def install_adf22bme(beam_species, target_ion, target_charge, transition, file_path, repository_path=None, adas_home=None):
-    pass
-    # """
-    # Adds the rate defined in an ADF21 file to the repository.
-    #
-    # :param file_path: Path relative to ADAS home.
-    # :param repository_path: Path to the repository in which to install the rates (optional).
-    # :param adas_home: Path to ADAS home directory (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_home: Path to ADAS home directory (optional).
+    """
 
     print('Installing {}...'.format(file_path))
     path = _locate_adas_file(file_path, adas_home)
@@ -313,6 +332,67 @@ def install_adf22bme(beam_species, target_ion, target_charge, transition, file_p
     repository.update_beam_emission_rates(rate, repository_path)
 
 
+def install_zeeman_structures(lines=None, adas_fort=None, repository_path=None):
+    """
+    Runs ADAS603 and adds Zeeman multiplet structures for given spectral lines to the repository.
+
+    :param lines: Spectral lines for which the Zeeman structure is calculated.
+        Run cherab.adas.adas6xx.print_adas603_supported_lines() to see the complete list
+        of supported lines.
+    :param adas_fort: Path to ADAS FORTRAN executables.
+        Default path is 'home/adas/bin64' for 64-bit systems or 'home/adas/bin' for 32-bit systems.
+    :param repository_path: Path to the repository in which to install the rates (optional).
+    """
+
+    if lines is None:
+        lines = ADAS603_SUPPORTED_LINES
+    else:
+        unsupported_lines = set(lines).difference(ADAS603_SUPPORTED_LINES)
+        if len(unsupported_lines):
+            unsupported_lines_str = '\n'.join([str(line) for line in unsupported_lines])
+            raise ValueError("The followoing spectral lines are not supported:\n{}".format(unsupported_lines_str))
+
+    zeeman_structures = RecursiveDict()
+    for line in lines:
+        data = run_adas603(line, adas_fort=adas_fort)
+        zeeman_structures[line.element][line.charge][line.transition] = data
+
+    repository.update_zeeman_structures(zeeman_structures, repository_path)
+
+
+def install_total_power_rate(element, uid='adas', year=96, repository_path=None):
+    """
+    Runs ADAS405 and adds total radiated power rate for given species to the repository.
+
+    :param element: Plasma species element.
+    :param uid: Username of adf11 location. Defaults to 'adas' for central ADAS data.
+    :param year: Year index of the adf11 data. Defaults to 96.
+    """
+
+    ne, te, _, total_power_rate, _, _, _, _ = run_adas405(uid=uid, year=year, elem=element.symbol.lower())
+    data = {'ne': ne, 'te': te, 'rate': total_power_rate}
+
+    repository.add_total_power_rate(element, data, repository_path=repository_path)
+
+
+def install_fractional_abundances(element, uid='adas', year=96, repository_path=None):
+    """
+    Runs ADAS405 and adds fractional abundances for given species to the repository.
+
+    :param element: Plasma species element.
+    :param uid: Username of adf11 location. Defaults to 'adas' for central ADAS data.
+    :param year: Year index of the adf11 data.
+    """
+
+    ne, te, fractionl_abundances, _, _, _, _, _ = run_adas405(uid=uid, year=year, elem=element.symbol.lower())
+    data = {element: {}}
+
+    for i in range(fractionl_abundances.shape[-1]):
+        data[element][i] = {'ne': ne, 'te': te, 'fractional_abundance': fractionl_abundances[:, :, i]}
+
+    repository.update_fractional_abundances(data, repository_path=repository_path)
+
+
 def _locate_adas_file(file_path, adas_home=None):
 
     path = None

cherab/adas/parse/__init__.py

@@ -1,6 +1,6 @@
-# Copyright 2016-2021 Euratom
-# Copyright 2016-2021 United Kingdom Atomic Energy Authority
-# Copyright 2016-2021 Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas
+# Copyright 2016-2023 Euratom
+# Copyright 2016-2023 United Kingdom Atomic Energy Authority
+# Copyright 2016-2023 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");