Implement iaea api

.devcontainer/devcontainer.json

@@ -0,0 +1,25 @@
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the
+// README at: https://github.com/devcontainers/templates/tree/main/src/python
+{
+	"name": "Python 3",
+	// Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile
+	"image": "mcr.microsoft.com/devcontainers/python:2-3.9-bullseye",
+	"features": {
+		"ghcr.io/devcontainers/features/python:1": {
+			"installTools": true,
+			"version": "3.9"
+		}
+	},
+
+	// Use 'forwardPorts' to make a list of ports inside the container available locally.
+	// "forwardPorts": [],
+
+	// Use 'postCreateCommand' to run commands after the container is created.
+	"postCreateCommand": "pip3 install --user -r requirements.txt"
+
+	// Configure tool-specific properties.
+	// "customizations": {},
+
+	// Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
+	// "remoteUser": "root"
+}

.github/workflows/renate-od.yml

@@ -5,15 +5,13 @@ on:
 
 jobs:
   build:
-
-    runs-on: ubuntu-20.04
-
+    runs-on: ubuntu-24.04
     steps:
     - uses: actions/checkout@v4
-    - name: Set up Python 3.6.4
+    - name: Set up Python 3.9.12
       uses: actions/setup-python@v5
       with:
-        python-version: '3.6.4'
+        python-version: '3.9.12'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
@@ -23,11 +21,11 @@ jobs:
         python -m unittest -v crm_solver.odetest.OdeTest
         python -m unittest -v crm_solver.crmsystemtest.CrmRegressionTest
         python -m unittest -v crm_solver.crmsystemtest.CrmAcceptanceTest
-        python -m unittest -v crm_solver.atomic_dbtest.AtomicDBTest
         python -m unittest -v crm_solver.beamlettest.BeamletTest
-        python -m unittest -v crm_solver.atomic_dbtest.RenateDBTest
-        python -m unittest -v crm_solver.neutral_dbtest.NeutralDBTest
         python -m unittest -v crm_solver.coefficientmatrixtest.CoefficientMatrixTest
+        python -m unittest -v atomic.atomic_dbtest.AtomicDBTest
+        python -m unittest -v atomic.atomic_dbtest.RenateDBTest
+        python -m unittest -v atomic.neutral_dbtest.NeutralDBTest
         python -m unittest -v utility.accessdatatest.AccessDataTest
         python -m unittest -v utility.getdatatest.GetDataTest
         python -m unittest -v utility.putdatatest.PutDataTest

atomic/aladdin.py

@@ -1,12 +1,95 @@
-# import requests
+import pycollisiondb
+from pycollisiondb.pycollisiondb import PyCollision
+from scipy.interpolate import interp1d
 
+class FitFunction(object):
+    def __init__(self, data):
+        self.coefficients = self.assign_from_fit(data, 'coeffs')
+        self.elo = self.assign_from_fit(data, 'Elo')
+        self.ehi = self.assign_from_fit(data, 'Ehi')
+        self.name = self.assign_from_fit(data, 'func')
+        self.precision = self.assign_from_fit(data, 'fit_unc_perc')
+
+    @staticmethod
+    def assign_from_fit(data, tag):
+        try:
+            return data[tag]
+        except KeyError:
+            return None
+
+class AladdinCrossSection(object):
+    def __init__(self, data):
+        if not isinstance(data, pycollisiondb.pycoll_ds.PyCollDataSet):
+            raise TypeError('The expected type from aladdin API is PyCollision')
+        self.energy = data.x
+        self.cross_section = data.y
+        self.len = data.n
+        self.reaction = self.assign_data(data, tag='reaction')
+        self.type = self.assign_data(data, tag='process_types')
+        self.uncertainty = float(self.assign_from_json(data, tag='unc_perc'))
+        #self.threshold = float(self.assign_from_json(data, tag='threshold'))
+        self.function = self.assign_from_json(data, tag='data_from_fit')
+        if self.function:
+            self.fit = FitFunction(data.metadata['json_data']['fit'])
+
+    @staticmethod
+    def assign_from_json(data, tag):
+        try:
+            return data.metadata['json_data'][tag]
+        except KeyError:
+            return None
+
+    @staticmethod
+    def assign_data(data, tag):
+        try:
+            return data.metadata[tag]
+        except KeyError:
+            return None
 
 class AladdinData(object):
-    def __init__(self):
-        pass
+    def __init__(self, url_source = 'aladdin'):
+        if isinstance(url_source, str):
+            if url_source == 'aladdin':
+                self.api_url = 'https://db-amdis.org/aladdin2/api/'
+            elif url_source == 'collisiondb':
+                self.api_url = 'https://db-amdis.org/collisiondb/api/'
+            else:
+                raise ValueError('The requested data source is not supported: ' + url_source)
+        else:
+            raise TypeError('The required data type for url specification is <str>.')
+
+    @staticmethod
+    def _set_sign(particle):
+        if particle.charge >= 1:
+            return '+'
+        else:
+            return '-'
+
+    def rod_to_pycoll(self, transition):
+        reactants = str(transition.projectile) + ' ' + transition.from_level + ' + ' + \
+                    str(transition.target) + self._set_sign(transition.target)
+
+        if transition.name == 'ex' or transition.name == 'de-ex':
+            products = str(transition.projectile) + ' ' + transition.to_level + ' + ' + \
+                       str(transition.target) + self._set_sign(transition.target)
+        elif transition.name == 'ion':
+            products = str(transition.projectile) + '+ + ' + \
+                       str(transition.target) + self._set_sign(transition.target) + ' + ' + 'e-'
+        elif transition.name == 'cx':
+            products = str(transition.projectile) + '+ + ' + \
+                       str(transition.target)
+        else:
+            products = str(transition.projectile) + '+ + '
+        return reactants + ' -> ' + products
 
-    def fetch_data(self, transition):
-        pass
+    def get_data_from_iaea(self, pycoll_reaction):
+        pycoll_raw = PyCollision.get_datasets(query = {'reaction_text':pycoll_reaction, 'data_type':'cross section'},
+                                              API_URL=self.api_url)
+        return AladdinCrossSection(pycoll_raw.datasets[list(pycoll_raw.datasets.keys())[0]])
 
-    def check_data(self, transition):
-        pass
+    def get_cross_section(self, transition, energy_grid):
+        reaction = self.rod_to_pycoll(transition)
+        aladdin_data = self.get_data_from_iaea(pycoll_reaction=reaction)
+        cross_function = interp1d(aladdin_data.energy, aladdin_data.cross_section,
+                                  kind='cubic', fill_value='extrapolate')
+        return cross_function(energy_grid)

atomic/cross_section.py

@@ -6,13 +6,13 @@
 
 class CrossSection:
 
-    CROSSEC_SOURCES = {'aladdin': [], 'internal': ['hydrogenic']}
+    CROSSEC_SOURCES = {'aladdin': [], 'collisiondb':[], 'internal': ['hydrogenic']}
 
     def __new__(cls, source, projectile=None):
         if not isinstance(source, str):
             raise TypeError('A string is expected to decide which data source to pursue.\n'+CrossSection.GetAvailableData())
-        if source == 'aladdin':
-            return AladdinData()
+        if source == 'aladdin' or source == 'collisiondb':
+            return AladdinData(url_source=source)
         elif source == 'internal':
             if not isinstance(projectile, str):
                 raise TypeError('The data source requires the projectile parameter to be a valid string.\n'+CrossSection.GetAvailableData())

atomic/internal_db.py

@@ -33,8 +33,20 @@ def __projectile_parameters(self):
                 self.projectile_particle = Particle(label='T', mass_number=3, atomic_number=1)
             self.atomic_dict = {'1': 0, '2': 1, '3': 2, '4': 3, '5': 4, '6': 5, None: None}
             self.atomic_levels = 6
-            self.inv_atomic_dict = {index: name for name, index in self.atomic_dict.items()}
-            self.mass = self.projectile_particle.mass
+        elif self.projectile == 'Li':
+            self.projectile_type = 'alkali'
+            self.projectile_particle = Particle(label='Li', charge=0, mass_number=7, atomic_number=3)
+            self.atomic_dict = {'2s': 0, '2p': 1, '3s': 2, '3p': 3, '3d': 4, '4s': 5, '4p': 6, '4d': 7, '4f': 8}
+            self.atomic_levels = 9
+        elif self.projectile == 'Na':
+            self.projectile_type = 'alkali'
+            self.projectile_particle = Particle(label='Na', charge=0, mass_number=23, atomic_number=11)
+            self.atomic_dict = {'3s': 0, '3p': 1, '3d': 2, '4s': 3, '4p': 4, '4d': 5, '4f': 6, '5s': 7}
+            self.atomic_levels = 8
+        else:
+            raise ValueError('The requested projectile is not yet supported.')
+        self.inv_atomic_dict = {index: name for name, index in self.atomic_dict.items()}
+        self.mass = self.projectile_particle.mass
 
     def _get_projectile_velocity(self):
         self.velocity = uc.calculate_velocity_from_energy(uc.convert_keV_to_eV(float(self.energy)), self.mass)
@@ -43,6 +55,10 @@ def _get_projectile_velocity(self):
     def set_default_atomic_levels(self):
         if self.projectile in ['H', 'D', 'T']:
             return '3', '2', '1', '3n-->2n'
+        elif self.projectile == 'Li':
+            return '2p', '2s', '2s', '2p-->2s'
+        elif self.projectile == 'Na':
+            return '3p', '3s', '3s', '3p-->3s'
 
     def get_rate_interpolator(self, reaction_type, target, from_level, to_level=None):
         #print(reaction_type, target, from_level, to_level)

crm_solver/beamlettest.py

@@ -8,7 +8,7 @@
 
 class BeamletTest(unittest.TestCase):
     EXPECTED_ATTR = ['param', 'components', 'profiles', 'coefficient_matrix', 'atomic_db', 'initial_condition']
-    EXPECTED_INITIAL_CONDITION = [4832583106.4753895, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
+    EXPECTED_INITIAL_CONDITION = [4832583046.75342, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
     EXPECTED_PARAM_ATTR = ['beamlet_source', 'beamlet_energy', 'beamlet_species', 'beamlet_current']
     EXPECTED_COMPONENTS_KEYS = ['q', 'Z', 'A']
     EXPECTED_COMPONENTS_SPECIES = ['electron', 'ion1', 'ion2']
@@ -42,8 +42,8 @@ def test_initial_conditions(self):
         for element in range(len(self.beamlet.initial_condition)):
             self.assertIsInstance(self.beamlet.initial_condition[element], float, msg='Expected type for initial'
                                                                                       ' conditions is float.')
-            self.assertEqual(self.beamlet.initial_condition[element], self.EXPECTED_INITIAL_CONDITION[element],
-                             msg='Computed Init conditions do not match expected init conditions.')
+            self.assertAlmostEqual(self.beamlet.initial_condition[element], self.EXPECTED_INITIAL_CONDITION[element],
+                             delta=1e-1, msg='Computed Init conditions do not match expected init conditions.')
 
     def test_param_xml(self):
         self.assertIsInstance(self.beamlet.param, etree._ElementTree,

requirements.txt

@@ -1,9 +1,10 @@
-scipy==1.0.0
-numpy==1.14.0
-pandas==0.22.0
-h5py==2.9.0
-matplotlib==2.1.2
-lxml==4.6.3
-tables==3.4.2
-paramiko==2.4.2
-scp==0.13.2
+scipy==1.8.0
+numpy==1.23.1
+pandas==1.4.2
+h5py==3.6.0
+matplotlib==3.6.0
+lxml==4.8.0
+tables==3.6.1
+paramiko==2.8.1
+scp==0.14.4
+pycollisiondb==0.1.3

utility/getdata.py

@@ -87,12 +87,8 @@ def read_h5_to_array(self):
             print('Data could NOT be read to array from HD5 file: ' + self.access_path + '. Key is missing!')
             raise ValueError
         try:
-            with h5py.File(self.access_path, 'r') as hdf5_id:
-                hdf5_group = hdf5_id
-                for key in self.data_key:
-                    hdf5_group = hdf5_group[key]
-                self.data = hdf5_group.value
-                hdf5_id.close()
+            with h5py.File(self.access_path, 'r') as file:
+                self.data = numpy.array(file[self.data_key[0]])
             print("Data read to array from HD5 file: " + self.access_path + " with key: " + str(self.data_key))
         except ValueError:
             print("Data could NOT be read to array from HD5 file: " + self.access_path +