Split the openadas module into atomic repository and OpenADAS parser

CHANGELOG.md

@@ -4,19 +4,31 @@ Project Changelog
 Release 1.5.0 (TBD)
 -------------------
 
+API changes:
+* Interpolated rates and local atomic repository functions are separated from OpenADAS parsers and installers and moved to cherab.atomic. (#364)
+* Default interface to atomic data repository is changed to cherab.atomic.AtomicData, as it includes the data beyond the frame of Open-ADAS. (#364)
+* The interface cherab.openadas.OpenADAS will continue to work as a wrapper for cherab.atomic.AtomicData for backward compatibility. (#364)
+* Default path to atomic data repository changed to `~/.cherab/atomicdata/default_repository`. Call populate() from cherab.atomic.repository after updating to 1.5.0 (#364)
+* InterpolatedFreeFreeGauntFactor and MaxwellianFreeFreeGauntFactor are replaced with a general interpolator FreeFreeGauntFactor from cherab.atomic.gaunt. (#364)
+* ZeemanStructure class is splitted to base (abstract) and interpolator classes. The latter is moved to cherab.atomic.zeeman and its initialiser interface is chaged to match the other atomic data interpolators. (#364)
+
 New:
 * Support Raysect 0.8
 * Add custom line shape support to BeamCXLine model. (#394)
+* Add functions to read/write free-free Gaunt factor in the atomic repository. (#364)
+* Add functions to read/write Zeeman structure in the atomic repository. (#364)
 * Add PeriodicTransformXD and VectorPeriodicTransformXD functions to support the data simulated with periodic boundary conditions. (#387)
 * Add CylindricalTransform and VectorCylindricalTransform to transform functions from cylindrical to Cartesian coordinates. (#387)
 * Add numerical integration of Bremsstrahlung spectrum over a spectral bin. (#395)
 * Replace the coarse numerical constant in the Bremsstrahlung model with an exact expression. (#409)
 * Add the kind attribute to RayTransferPipelineXD that determines whether the ray transfer matrix is multiplied by sensitivity ('power') or not ('radiance'). (#412)
 * Improved parsing of metadata from the ADAS ADF15 'bnd' files for H-like ions. Raises a runtime error if the metadata cannot be parsed. (#424)
+* Get the path to the default atomic data repository from the CHERAB_ATOMIC_DATA environment variable. (#416)
 
 Bug fixes:
 * Fix deprecated transforms being cached in LaserMaterial after laser.transform update (#420)
 
+
 Release 1.4.0 (3 Feb 2023)
 -------------------
 

cherab/atomic/__init__.py

@@ -0,0 +1,20 @@
+# Copyright 2016-2022 Euratom
+# Copyright 2016-2022 United Kingdom Atomic Energy Authority
+# Copyright 2016-2022 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");
+# You may not use this work except in compliance with the Licence.
+# You may obtain a copy of the Licence at:
+#
+# https://joinup.ec.europa.eu/software/page/eupl5
+#
+# Unless required by applicable law or agreed to in writing, software distributed
+# under the Licence is distributed on an "AS IS" basis, WITHOUT WARRANTIES OR
+# CONDITIONS OF ANY KIND, either express or implied.
+#
+# See the Licence for the specific language governing permissions and limitations
+# under the Licence.
+
+from . import repository
+from .atomicdata import AtomicData

cherab/atomic/gaunt/__init__.pxd

@@ -0,0 +1,19 @@
+# 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");
+# You may not use this work except in compliance with the Licence.
+# You may obtain a copy of the Licence at:
+#
+# https://joinup.ec.europa.eu/software/page/eupl5
+#
+# Unless required by applicable law or agreed to in writing, software distributed
+# under the Licence is distributed on an "AS IS" basis, WITHOUT WARRANTIES OR
+# CONDITIONS OF ANY KIND, either express or implied.
+#
+# See the Licence for the specific language governing permissions and limitations
+# under the Licence.
+
+from cherab.atomic.gaunt.gaunt cimport *

cherab/atomic/gaunt/__init__.py

@@ -0,0 +1,19 @@
+# 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");
+# You may not use this work except in compliance with the Licence.
+# You may obtain a copy of the Licence at:
+#
+# https://joinup.ec.europa.eu/software/page/eupl5
+#
+# Unless required by applicable law or agreed to in writing, software distributed
+# under the Licence is distributed on an "AS IS" basis, WITHOUT WARRANTIES OR
+# CONDITIONS OF ANY KIND, either express or implied.
+#
+# See the Licence for the specific language governing permissions and limitations
+# under the Licence.
+
+from .gaunt import FreeFreeGauntFactor

cherab/atomic/gaunt/gaunt.pxd

@@ -0,0 +1,29 @@
+# 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");
+# You may not use this work except in compliance with the Licence.
+# You may obtain a copy of the Licence at:
+#
+# https://joinup.ec.europa.eu/software/page/eupl5
+#
+# Unless required by applicable law or agreed to in writing, software distributed
+# under the Licence is distributed on an "AS IS" basis, WITHOUT WARRANTIES OR
+# CONDITIONS OF ANY KIND, either express or implied.
+#
+# See the Licence for the specific language governing permissions and limitations
+# under the Licence.
+
+from cherab.core.math cimport Function2D
+from cherab.core.atomic cimport FreeFreeGauntFactor as CoreFreeFreeGauntFactor
+
+
+cdef class FreeFreeGauntFactor(CoreFreeFreeGauntFactor):
+
+    cdef:
+        readonly tuple u_range, gamma2_range
+        readonly dict raw_data
+        double _u_min, _u_max, _gamma2_min, _gamma2_max
+        Function2D _gaunt_factor

cherab/atomic/gaunt/gaunt.pyx

@@ -0,0 +1,104 @@
+# 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");
+# You may not use this work except in compliance with the Licence.
+# You may obtain a copy of the Licence at:
+#
+# https://joinup.ec.europa.eu/software/page/eupl5
+#
+# Unless required by applicable law or agreed to in writing, software distributed
+# under the Licence is distributed on an "AS IS" basis, WITHOUT WARRANTIES OR
+# CONDITIONS OF ANY KIND, either express or implied.
+#
+# See the Licence for the specific language governing permissions and limitations
+# under the Licence.
+
+import numpy as np
+from libc.math cimport log10, log, M_PI, sqrt
+from raysect.core.math.function.float cimport Interpolator2DArray
+from cherab.core.utility.constants cimport RYDBERG_CONSTANT_EV, SPEED_OF_LIGHT, ELEMENTARY_CHARGE, PLANCK_CONSTANT
+
+cimport cython
+
+
+DEF EULER_GAMMA = 0.5772156649015329
+
+cdef double PH_TO_EV_FACTOR = PLANCK_CONSTANT * SPEED_OF_LIGHT * 1e9 / ELEMENTARY_CHARGE
+
+
+cdef class FreeFreeGauntFactor(CoreFreeFreeGauntFactor):
+    r"""
+    The temperature-averaged free-free Gaunt factors interpolated in the space of parameters:
+    :math:`u = h{\nu}/kT` and :math:`{\gamma}^{2} = Z^{2}Ry/kT`.
+    See T.R. Carson, 1988, Astron. & Astrophys., 189,
+    `319 <https://ui.adsabs.harvard.edu/#abs/1988A&A...189..319C/abstract>`_ for details.
+
+    The cubic interpolation in a semi-log space is used.
+
+    The Born approximation and classical limits are used outside the interpolation range.
+
+    :param dict data: Dictionary containing the Gaunt factor data with the following keys:
+
+    |      'u': A 1D array of real values.
+    |      'gamma2': A 1D array of real values.
+    |      'gaunt_factor': 2D array of real values storing the Gaunt factor values at u, gamma2.
+
+    :ivar tuple u_range: The interpolation range of `u` parameter.
+    :ivar tuple gamma2_range: The interpolation range of :math:`\\gamma^2` parameter.
+    :ivar dict raw_data: Dictionary containing the raw data.
+    """
+
+    def __init__(self, dict data):
+
+        self.raw_data = data
+
+        u = data['u']
+        gamma2 = data['gamma2']
+        gaunt_factor = data['gaunt_factor']
+
+        self._u_min = u.min()
+        self._u_max = u.max()
+        self._gamma2_min = gamma2.min()
+        self._gamma2_max = gamma2.max()
+
+        self.u_range = (self._u_min, self._u_max)
+        self.gamma2_range = (self._gamma2_min, self._gamma2_max)
+
+        self._gaunt_factor = Interpolator2DArray(np.log10(u), np.log10(gamma2), gaunt_factor, 'cubic', 'none', 0, 0)
+
+    @cython.cdivision(True)
+    cpdef double evaluate(self, double z, double temperature, double wavelength) except? -1e999:
+        """
+        Returns the temperature-averaged free-free Gaunt factor for the supplied parameters.
+
+        :param double z: Species charge or effective plasma charge.
+        :param double temperature: Electron temperature in eV.
+        :param double wavelength: Spectral wavelength.
+
+        :return: free-free Gaunt factor
+        """
+
+        cdef:
+            double u, gamma2
+
+        if z == 0:
+
+            return 0
+
+        gamma2 = z * z * RYDBERG_CONSTANT_EV / temperature
+        u = PH_TO_EV_FACTOR / (temperature * wavelength)
+
+        # classical limit
+        if u >= self._u_max or gamma2 >= self._gamma2_max:
+
+            return 1
+
+        # Born approximation limit
+        if u < self._u_min or gamma2 < self._gamma2_min:
+
+            return sqrt(3) / M_PI * (log(4 / u) - EULER_GAMMA)
+
+        return self._gaunt_factor.evaluate(log10(u), log10(gamma2))

cherab/atomic/rates/__init__.pxd

@@ -0,0 +1,24 @@
+# Copyright 2016-2022 Euratom
+# Copyright 2016-2022 United Kingdom Atomic Energy Authority
+# Copyright 2016-2022 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");
+# You may not use this work except in compliance with the Licence.
+# You may obtain a copy of the Licence at:
+#
+# https://joinup.ec.europa.eu/software/page/eupl5
+#
+# Unless required by applicable law or agreed to in writing, software distributed
+# under the Licence is distributed on an "AS IS" basis, WITHOUT WARRANTIES OR
+# CONDITIONS OF ANY KIND, either express or implied.
+#
+# See the Licence for the specific language governing permissions and limitations
+# under the Licence.
+
+from cherab.atomic.rates.beam cimport *
+from cherab.atomic.rates.cx cimport *
+from cherab.atomic.rates.pec cimport *
+from cherab.atomic.rates.atomic cimport *
+from cherab.atomic.rates.radiated_power cimport *
+from cherab.atomic.rates.fractional_abundance cimport *

cherab/atomic/rates/__init__.py

@@ -0,0 +1,24 @@
+# Copyright 2016-2018 Euratom
+# Copyright 2016-2018 United Kingdom Atomic Energy Authority
+# Copyright 2016-2018 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");
+# You may not use this work except in compliance with the Licence.
+# You may obtain a copy of the Licence at:
+#
+# https://joinup.ec.europa.eu/software/page/eupl5
+#
+# Unless required by applicable law or agreed to in writing, software distributed
+# under the Licence is distributed on an "AS IS" basis, WITHOUT WARRANTIES OR
+# CONDITIONS OF ANY KIND, either express or implied.
+#
+# See the Licence for the specific language governing permissions and limitations
+# under the Licence.
+
+from .beam import *
+from .cx import *
+from .pec import *
+from .atomic import *
+from .radiated_power import *
+from .fractional_abundance import *