Feature/ionbalance

MANIFEST.in

@@ -0,0 +1,4 @@
+include README.md CHANGELOG.md LICENSE.txt MANIFEST.in setup.py .gitignore
+recursive-include cherab *.py *.pyx *.pxd *.json
+recursive-include demos *.py *.pyx *.pxd
+

cherab/openadas/config.py

@@ -136,7 +136,7 @@ def _check_for_adf_file(open_adas_root_path, relative_adf_file_path, download_pa
 for element, ionisation, relative_adf_path, download_path in DEFAULT_ADF15_FILES:
     print(relative_adf_path)
     _check_for_adf_file(ROOT_DATA_PATH, relative_adf_path, download_path)
-    add_adf15_to_atomic_data(default, element, ionisation, os.path.join(ROOT_DATA_PATH, relative_adf_path))
+    default = add_adf15_to_atomic_data(default, element, ionisation, os.path.join(ROOT_DATA_PATH, relative_adf_path))
 
 # TODO: there are concerns about the accuracy of this data
 # Data from NIST Atomic Spectra Database - http://www.nist.gov/pml/data/asd.cfm

cherab/openadas/library/__init__.py

@@ -0,0 +1,18 @@
+# Copyright 2014-2017 United Kingdom Atomic Energy Authority
+#
+# 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 .library import ADF11_PLT_FILES, ADF11_PRB_FILES

cherab/openadas/library/adf11.json

@@ -0,0 +1,87 @@
+{
+  "Description": "Recommended set of ADF11 files for PLT coefficients",
+  "adf11_plt_files": {
+    "H": {
+      "ADAS_Path": "adf11/plt12/plt12_h.dat",
+      "Download_URL": "http://open.adas.ac.uk/download/adf11/plt12/plt12_h.dat"
+    },
+    "He": {
+      "ADAS_Path": "adf11/plt96/plt96_he.dat",
+      "Download_URL": "http://open.adas.ac.uk/download/adf11/plt96/plt96_he.dat"
+    },
+    "Li": {
+      "ADAS_Path": "adf11/plt96/plt96_li.dat",
+      "Download_URL": "http://open.adas.ac.uk/download/adf11/plt96/plt96_li.dat"
+    },
+    "Be": {
+    "ADAS_Path": "adf11/plt96/plt96_be.dat",
+    "Download_URL": "http://open.adas.ac.uk/download/adf11/plt96/plt96_be.dat"
+    },
+    "C": {
+    "ADAS_Path": "adf11/plt96/plt96_c.dat",
+    "Download_URL": "http://open.adas.ac.uk/download/adf11/plt96/plt96_c.dat"
+    },
+    "N": {
+    "ADAS_Path": "adf11/plt96/plt96_n.dat",
+    "Download_URL": "http://open.adas.ac.uk/download/adf11/plt96/plt96_n.dat"
+    },
+    "O": {
+      "ADAS_Path": "adf11/plt96/plt96_o.dat",
+      "Download_URL": "http://open.adas.ac.uk/download/adf11/plt96/plt96_o.dat"
+    },
+    "Ne": {
+      "ADAS_Path": "adf11/plt96/plt96_ne.dat",
+      "Download_URL": "http://open.adas.ac.uk/download/adf11/plt96/plt96_ne.dat"
+    },
+    "Ar": {
+    "ADAS_Path": "adf11/plt40/plt40_ar.dat",
+    "Download_URL": "http://open.adas.ac.uk/download/adf11/plt40/plt40_ar.dat"
+    },
+    "Kr": {
+      "ADAS_Path": "adf11/plt89/plt89_kr.dat",
+      "Download_URL": "http://open.adas.ac.uk/download/adf11/plt89/plt89_kr.dat"
+    }
+  },
+  "adf11_prb_files": {
+    "H": {
+      "ADAS_Path": "adf11/prb12/prb12_h.dat",
+      "Download_URL": "http://open.adas.ac.uk/download/adf11/prb12/prb12_h.dat"
+    },
+    "He": {
+      "ADAS_Path": "adf11/prb96/prb96_he.dat",
+      "Download_URL": "http://open.adas.ac.uk/download/adf11/prb96/prb96_he.dat"
+    },
+    "Li": {
+      "ADAS_Path": "adf11/prb96/prb96_li.dat",
+      "Download_URL": "http://open.adas.ac.uk/download/adf11/prb96/prb96_li.dat"
+    },
+    "Be": {
+      "ADAS_Path": "adf11/prb96/prb96_be.dat",
+      "Download_URL": "http://open.adas.ac.uk/download/adf11/prb96/prb96_be.dat"
+    },
+    "C": {
+      "ADAS_Path": "adf11/prb96/prb96_c.dat",
+      "Download_URL": "http://open.adas.ac.uk/download/adf11/prb96/prb96_c.dat"
+    },
+    "N": {
+      "ADAS_Path": "adf11/prb96/prb96_n.dat",
+      "Download_URL": "http://open.adas.ac.uk/download/adf11/prb96/prb96_n.dat"
+    },
+    "O": {
+      "ADAS_Path": "adf11/prb96/prb96_o.dat",
+      "Download_URL": "http://open.adas.ac.uk/download/adf11/prb96/prb96_o.dat"
+    },
+    "Ne": {
+      "ADAS_Path": "adf11/prb96/prb96_ne.dat",
+      "Download_URL": "http://open.adas.ac.uk/download/adf11/prb96/prb96_ne.dat"
+    },
+    "Ar": {
+      "ADAS_Path": "adf11/prb89/prb89_ar.dat",
+      "Download_URL": "http://open.adas.ac.uk/download/adf11/prb89/prb89_ar.dat"
+    },
+    "Kr": {
+      "ADAS_Path": "adf11/prb89/prb89_kr.dat",
+      "Download_URL": "http://open.adas.ac.uk/download/adf11/prb89/prb89_kr.dat"
+    }
+  }
+}

cherab/openadas/library/library.py

@@ -0,0 +1,29 @@
+# Copyright 2014-2017 United Kingdom Atomic Energy Authority
+#
+# 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 os
+import json
+
+
+LIBRARY_PATH = os.path.split(__file__)[0]
+
+ADF11_FILES = json.load(open(os.path.join(LIBRARY_PATH, 'adf11.json')))
+ADF11_PLT_FILES = ADF11_FILES['adf11_plt_files']
+ADF11_PRB_FILES = ADF11_FILES['adf11_prb_files']
+
+
+

cherab/openadas/openadas.py

@@ -15,14 +15,18 @@
 # under the Licence.
 
 import os
+import urllib.request
 
-from cherab.core import AtomicData, Isotope
+from cherab.core import AtomicData
 from cherab.core.atomic.elements import Isotope
-from pkg_resources import resource_filename
+from cherab.core.utility.recursivedict import RecursiveDict
 
-from cherab.openadas.read import adf12, adf15, adf21, adf22
+from cherab.openadas.library import *
+from cherab.openadas.read import adf11, adf12, adf15, adf21, adf22
+from cherab.openadas.read.adf15 import add_adf15_to_atomic_data
 from . import config
 from .rates import *
+from cherab.openadas.rates.radiated_power import StageResolvedRadiation
 
 
 class OpenADAS(AtomicData):
@@ -32,8 +36,7 @@ def __init__(self, data_path=None, config=config.default, permit_extrapolation=F
         super().__init__()
         self._data_path = data_path or self._setup_data_path()
 
-        # configuration is immutable, changes to ADAS state are not tracked
-        self._config = config.copy()
+        self._config = config
 
         # if true informs interpolation objects to allow extrapolation beyond the limits of the tabulated data
         self._permit_extrapolation = permit_extrapolation
@@ -208,3 +211,69 @@ def recombination_rate(self, ion, ionisation, transition):
         data = adf15(os.path.join(self._data_path, filename), block_number)
         return RecombinationRate(wavelength, data, extrapolate=self._permit_extrapolation)
 
+    def stage_resolved_line_radiation_rate(self, ion, ionisation):
+
+        # extract element from isotope
+        if isinstance(ion, Isotope):
+            ion = ion.element
+
+        try:
+            plt_files = ADF11_PLT_FILES[ion.symbol]
+        except KeyError:
+            raise ValueError("No ADF11 files set for Ion - {}".format(ion.symbol))
+
+        absolute_file_path = self._check_for_adf_file(plt_files['ADAS_Path'], plt_files['Download_URL'])
+
+        densities, temperatures, rate_data = adf11(absolute_file_path, ion, ionisation)
+
+        name = 'Stage Resolved Line Radiation - ({}, {})'.format(ion.symbol, ionisation)
+        return StageResolvedRadiation(ion, ionisation, densities, temperatures, rate_data,
+                                      name=name, extrapolate=self._permit_extrapolation)
+
+    def stage_resolved_continuum_radiation_rate(self, ion, ionisation):
+
+        # extract element from isotope
+        if isinstance(ion, Isotope):
+            ion = ion.element
+
+        try:
+            prb_files = ADF11_PRB_FILES[ion.symbol]
+        except KeyError:
+            raise ValueError("No ADF11 files set for Ion - {}".format(ion.symbol))
+
+        absolute_file_path = self._check_for_adf_file(prb_files['ADAS_Path'], prb_files['Download_URL'])
+
+        densities, temperatures, rate_data = adf11(absolute_file_path, ion, ionisation)
+
+        name = 'Stage Resolved Continuum Radiation - ({}, {})'.format(ion.symbol, ionisation)
+
+        return StageResolvedRadiation(ion, ionisation, densities, temperatures, rate_data,
+                                      name=name, extrapolate=self._permit_extrapolation)
+
+    def _check_for_adf_file(self, relative_adf_file_path, download_path):
+
+        relative_adf_directory, adf_file_name = os.path.split(relative_adf_file_path)
+        absolute_adf_directory = os.path.join(self._data_path, relative_adf_directory)
+        absolute_file_path = os.path.join(absolute_adf_directory, adf_file_name)
+
+        if not os.path.exists(absolute_adf_directory):
+            os.makedirs(absolute_adf_directory)
+
+        if os.path.isfile(absolute_file_path):
+            return absolute_file_path
+        else:
+            urllib.request.urlretrieve(download_path, absolute_file_path)
+
+        return absolute_file_path
+
+    def add_adf15_file(self, element, ionisation, adf_file_path):
+
+        if not os.path.isfile(adf_file_path):
+            new_path = os.path.join(os.path.expanduser('~/.cherab/openadas'), adf_file_path)
+            if not os.path.isfile(new_path):
+                raise ValueError("Could not find ADF15 file - '{}'".format(adf_file_path))
+            adf_file_path = new_path
+
+        atomic_data_dict = RecursiveDict.from_dict(self._config)
+        atomic_data_dict = add_adf15_to_atomic_data(atomic_data_dict, element, ionisation, adf_file_path)
+        self._config = atomic_data_dict.freeze()

cherab/openadas/rates/pec.pyx

@@ -42,7 +42,14 @@ cdef class ImpactExcitationRate(CoreImpactExcitationRate):
         )
 
     cpdef double evaluate(self, double density, double temperature) except? -1e999:
-        return self._pec.evaluate(density, temperature)
+
+        cdef double rate
+
+        rate = self._pec.evaluate(density, temperature)
+        if rate < 0:
+            return 0.0
+
+        return rate
 
 
 # todo: evaluate it the interpolation can be done without the log10 operations? or if this should be ported to the cx rates.
@@ -66,7 +73,14 @@ cdef class RecombinationRate(CoreRecombinationRate):
 
 
     cpdef double evaluate(self, double density, double temperature) except? -1e999:
-        return self._pec.evaluate(density, temperature)
+
+        cdef double rate
+
+        rate = self._pec.evaluate(density, temperature)
+        if rate < 0:
+            return 0.0
+
+        return rate
 
 
 # cdef class ThermalCXRate(CoreThermalCXRate):

cherab/openadas/rates/radiated_power.pyx

@@ -0,0 +1,58 @@
+
+# Copyright 2014-2017 United Kingdom Atomic Energy Authority
+#
+# 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 numpy cimport ndarray
+from cherab.core.math.interpolators.interpolators2d cimport Interpolate2DCubic
+from cherab.core.atomic.rates cimport StageResolvedLineRadiation as CoreStageResolvedLineRadiation
+
+
+cdef class StageResolvedRadiation(CoreStageResolvedLineRadiation):
+
+    cdef:
+        readonly bint extrapolate
+        readonly tuple density_range, temperature_range
+        readonly ndarray _electron_density, _electron_temperature, _radiated_power
+        readonly Interpolate2DCubic _power_func
+
+    def __init__(self, element, ionisation, electron_density, electron_temperature, radiated_power, name='', extrapolate=False):
+
+        super().__init__(element, ionisation, name=name)
+
+        self._electron_density = np.array(electron_density, dtype=np.float64)
+        self._electron_temperature = np.array(electron_temperature, dtype=np.float64)
+        self._radiated_power = np.array(radiated_power, dtype=np.float64)
+
+        if not all(j >= 0 for i in self._radiated_power for j in i):
+            raise ValueError("Can't have negative power values!")
+
+        self.density_range = (self._electron_density.min(), self._electron_density.max())
+        self.temperature_range = (self._electron_temperature.min(), self._electron_temperature.max())
+
+        self.extrapolate = extrapolate
+        self._power_func = Interpolate2DCubic(self._electron_density, self._electron_temperature, self._radiated_power,
+                                              extrapolate=extrapolate, extrapolation_type="nearest")
+
+    cdef double evaluate(self, double electron_density, double electron_temperature) except? -1e999:
+        cdef double rate
+        rate = self._power_func.evaluate(electron_density, electron_temperature)
+        if rate < 0:
+            print("Warning - negative power encountered!")
+            print("ne - {:.4G}, te - {:.3G}, rate - {:.4G}".format(electron_density, electron_temperature, rate))
+        return rate
+        # return self._power_func.evaluate(electron_density, electron_temperature)
+

cherab/openadas/read/__init__.py

@@ -15,6 +15,7 @@
 # under the Licence.
 
 
+from .adf11 import adf11
 from .adf12 import adf12
 from .adf15 import adf15
 from .adf21 import adf21