Change to NLTE properties

tardis/plasma/base.py

@@ -108,7 +108,12 @@ def _init_properties(self, plasma_properties, **kwargs):
         self.outputs_dict = {}
         for plasma_property in plasma_properties:
 
-            if hasattr(plasma_property, 'set_value'):
+            if hasattr(plasma_property, 'set_initial_value'):
+                #duck-typing for PreviousIterationProperty
+                current_property_object = plasma_property()
+                current_property_object.set_initial_value(kwargs)
+
+            elif hasattr(plasma_property, 'set_value'):
                 #duck-typing for PlasmaInputProperty
                 #that means if it is an input property from model
                 if not set(kwargs.keys()).issuperset(plasma_property.outputs):

tardis/plasma/properties/general.py

@@ -48,7 +48,8 @@ class NumberDensity(ProcessingPlasmaProperty):
     outputs = ('number_density',)
     latex_name = ('N_{i}',)
 
-    def calculate(self, atomic_mass, abundance, density):
+    @staticmethod
+    def calculate(atomic_mass, abundance, density):
         number_densities = (abundance * density)
         return number_densities.div(atomic_mass.ix[abundance.index], axis=0)
 

tardis/plasma/properties/nlte.py

@@ -5,11 +5,16 @@
 from tardis.plasma.properties.base import (BasePlasmaProperty,
                                            ProcessingPlasmaProperty)
 from tardis.plasma.properties import PhiSahaNebular, PhiSahaLTE
+from tardis.plasma.properties import NumberDensity
 
 __all__ = ['PreviousElectronDensities', 'PreviousBetaSobolevs',
            'HeliumNLTE']
 
 class PreviousIterationProperty(BasePlasmaProperty):
+
+    def _set_initial_value(self, value):
+        self.set_value(value)
+
     def _set_output_value(self, output, value):
         setattr(self, output, value)
 
@@ -20,9 +25,22 @@ def set_value(self, value):
 class PreviousElectronDensities(PreviousIterationProperty):
     outputs = ('previous_electron_densities',)
 
+    def set_initial_value(self, kwargs):
+        initial_value = np.ones(len(kwargs['abundance'].columns))*1000000.0
+        self._set_initial_value(initial_value)
+
 class PreviousBetaSobolevs(PreviousIterationProperty):
     outputs = ('previous_beta_sobolevs',)
 
+    def set_initial_value(self, kwargs):
+        try:
+            lines = len(kwargs['atomic_data'].lines)
+        except:
+            lines = len(kwargs['atomic_data']._lines)
+        initial_value = np.ones((lines,
+            len(kwargs['abundance'].columns)))
+        self._set_initial_value(initial_value)
+
 class HeliumNLTE(ProcessingPlasmaProperty):
     outputs = ('helium_population',)
 

tardis/plasma/properties/property_collections.py

@@ -1,16 +1,4 @@
-from tardis.plasma.properties import (BetaRadiation, LevelBoltzmannFactorLTE,
-    Levels, Lines, AtomicMass, PartitionFunction,
-    LevelNumberDensity, PhiSahaLTE, GElectron,
-    IonizationData, NumberDensity, IonNumberDensity, LinesLowerLevelIndex,
-    LinesUpperLevelIndex, TauSobolev, TRadiative, AtomicData, Abundance,
-    Density, TimeExplosion, BetaSobolev, JBlues,
-    TransitionProbabilities, StimulatedEmissionFactor, SelectedAtoms,
-    PhiSahaNebular, LevelBoltzmannFactorDiluteLTE, DilutionFactor,
-    ZetaData, ElectronTemperature, LinkTRadTElectron, BetaElectron,
-    RadiationFieldCorrection, RadiationFieldCorrectionInput,
-    LevelBoltzmannFactorNoNLTE, LevelBoltzmannFactorNLTE, NLTEData,
-    NLTESpecies, PreviousBetaSobolevs, LTEJBlues,
-    PreviousElectronDensities, Chi0, HeliumNLTE)
+from tardis.plasma.properties import *
 
 class PlasmaPropertyCollection(list):
     pass

tardis/plasma/standard_plasmas.py

@@ -24,8 +24,7 @@ def __init__(self, t_rad, abundance, density, time_explosion, atomic_data,
             t_rad=t_rad, abundance=abundance, atomic_data=atomic_data,
             density=density, time_explosion=time_explosion, j_blues=j_blues,
 	        w=None, link_t_rad_t_electron=link_t_rad_t_electron,
-            delta_input=delta_treatment, nlte_species=None,
-            previous_beta_sobolevs=None, previous_electron_densities=None)
+            delta_input=delta_treatment, nlte_species=None)
 
 class LegacyPlasmaArray(BasePlasma):
 
@@ -112,6 +111,4 @@ def __init__(self, number_densities, atomic_data, time_explosion,
             t_rad=t_rad, abundance=abundance, density=density,
             atomic_data=atomic_data, time_explosion=time_explosion,
             j_blues=None, w=w, link_t_rad_t_electron=link_t_rad_t_electron,
-            delta_input=delta_treatment, nlte_species=nlte_species,
-            previous_electron_densities=initial_electron_densities,
-            previous_beta_sobolevs=initial_beta_sobolevs)
+            delta_input=delta_treatment, nlte_species=nlte_species)