Revert "Plasma restructure"

conda-requirements

@@ -8,5 +8,4 @@ astropy>=0.4
 PyYAML>=3.0
 numexpr>=2.0.0
 Cython>=0.21
-jinja2
-networkx
+jinja2

tardis/atomic.py

@@ -358,20 +358,12 @@ def from_hdf5(cls, fname=None):
     def __init__(self, atom_data, ionization_data, levels_data, lines_data, macro_atom_data=None, zeta_data=None,
                  collision_data=None, synpp_refs=None, ion_cx_data=None):
 
-        if levels_data is not None:
-            self.has_levels = True
-        else:
-            self.has_levels = False
-
-        if lines_data is not None:
-            self.has_lines = True
-        else:
-            self.has_lines = False
 
         if macro_atom_data is not None:
             self.has_macro_atom = True
             self.macro_atom_data_all = DataFrame(macro_atom_data[0].__array__())
             self.macro_atom_references_all = DataFrame(macro_atom_data[1].__array__())
+
         else:
             self.has_macro_atom = False
 
@@ -439,7 +431,7 @@ def __init__(self, atom_data, ionization_data, levels_data, lines_data, macro_at
 
 
 
-        self.ion_cx_data = ion_cx_data
+
 
 
 

tardis/conftest.py

@@ -139,35 +139,4 @@ def pytest_report_header(config):
     if not six.PY3:
         s = s.encode(stdoutencoding, 'replace')
 
-    return s
-
-
-import os
-
-@pytest.fixture
-def atomic_data_fname():
-    atomic_data_fname = pytest.config.getvalue("atomic-dataset")
-    if atomic_data_fname is None:
-        pytest.skip('--atomic_database was not specified')
-    else:
-        return os.path.expandvars(os.path.expanduser(atomic_data_fname))
-
-from tardis.atomic import AtomData
-
-@pytest.fixture
-def kurucz_atomic_data(atomic_data_fname):
-    atomic_data = AtomData.from_hdf5(atomic_data_fname)
-
-    if atomic_data.md5 != '21095dd25faa1683f4c90c911a00c3f8':
-        pytest.skip('Need default Kurucz atomic dataset '
-                    '(md5="21095dd25faa1683f4c90c911a00c3f8"')
-    else:
-        return atomic_data
-
-@pytest.fixture
-def included_he_atomic_data():
-    import os, tardis
-    atomic_db_fname = os.path.join(tardis.__path__[0], 'tests', 'data',
-                                   'chianti_he_db.h5')
-    return AtomData.from_hdf5(atomic_db_fname)
-
+    return s

tardis/data/lucy99_general_default.ini

@@ -0,0 +1,12 @@
+[general]
+max_atom=30
+max_ion=30
+time_exp=13
+v_inner=11000.0
+v_outer=30000.0
+log_l_lsun=9.44
+zones=20
+calibration_packets=2e4
+spectrum_packets=1e5
+iterations=10
+density_model=lucy99_w7

tardis/data/tardis_config_definition.yml

@@ -85,7 +85,7 @@ plasma:
         property_type: string
         mandatory: True
         default: None
-        allowed_value: dilute-blackbody detailed blackbody
+        allowed_value: dilute-blackbody detailed
         help: radiative rates treatment mode
 
     line_interaction_type:

tardis/io/tests/test_model_reader.py

@@ -1,35 +1,38 @@
-import os
+import tardis
+from tardis.io.model_reader import (read_artis_density,
+read_simple_ascii_abundances)
 
 from astropy import units as u
 import numpy as np
+
 import pytest
 
-import tardis
-from tardis.io.model_reader import (read_artis_density, 
-read_simple_ascii_abundances)
+import os
 
 data_path = os.path.join(tardis.__path__[0], 'io', 'tests', 'data')
 
 @pytest.fixture
 def artis_density_fname():
     return os.path.join(data_path, 'artis_model.dat')
-
 @pytest.fixture
 def artis_abundances_fname():
     return os.path.join(data_path, 'artis_abundances.dat')
 
 def test_simple_read_artis_density(artis_density_fname):
     (time_of_model, index, v_inner, v_outer,
-        mean_density) = read_artis_density(artis_density_fname)
+     mean_density) = read_artis_density(artis_density_fname)
 
     assert np.isclose(0.00114661 * u.day, time_of_model, atol=1e-7 * u.day)
-    assert np.isclose(mean_density[23], 0.2250048 * u.g / u.cm**3, atol=1.e-6
-        * u.g / u.cm**3)
+    assert np.isclose(mean_density[23], 0.2250048 * u.g / u.cm**3, atol=1.e-6 * 
+        u.g / u.cm**3)
     assert len(mean_density) == 69
     assert len(mean_density) == len(v_inner)
 
-# Artis files are currently read with read ascii files function
+#Artis files are currently read with read ascii files function
 def test_read_simple_ascii_abundances(artis_abundances_fname):
     index, abundances = read_simple_ascii_abundances(artis_abundances_fname)
     assert len(abundances.columns) == 69
     assert np.isclose(abundances[23].ix[2], 2.672351e-08 , atol=1.e-12)
+
+
+

tardis/model.py

@@ -10,10 +10,9 @@
 import scipy.special
 
 from util import intensity_black_body
-from tardis import packet_source
+from tardis import packet_source, plasma_array
 from tardis.montecarlo import montecarlo
 from tardis.montecarlo.base import MontecarloRunner
-from tardis.plasma.standard_plasmas import LegacyPlasmaArray
 
 
 
@@ -122,14 +121,16 @@ def __init__(self, tardis_config):
         self.ws = (0.5 * (1 - np.sqrt(1 -
                     (tardis_config.structure.r_inner[0] ** 2 / tardis_config.structure.r_middle ** 2).to(1).value)))
 
-        self.plasma_array = LegacyPlasmaArray(tardis_config.number_densities, tardis_config.atom_data,
+
+        self.plasma_array = plasma_array.BasePlasmaArray(tardis_config.number_densities, tardis_config.atom_data,
                                                          tardis_config.supernova.time_explosion.to('s').value,
                                                          nlte_config=tardis_config.plasma.nlte,
                                                          delta_treatment=tardis_config.plasma.delta_treatment,
                                                          ionization_mode=tardis_config.plasma.ionization,
-                                                         excitation_mode=tardis_config.plasma.excitation,
-                                                         line_interaction_type=tardis_config.plasma.line_interaction_type,
-                                                         link_t_rad_t_electron=0.9)
+                                                         excitation_mode=tardis_config.plasma.excitation)
+
+
+
 
         self.spectrum = TARDISSpectrum(tardis_config.spectrum.frequency, tardis_config.supernova.distance)
         self.spectrum_virtual = TARDISSpectrum(tardis_config.spectrum.frequency, tardis_config.supernova.distance)
@@ -176,7 +177,7 @@ def calculate_j_blues(self, init_detailed_j_blues=False):
         radiative_rates_type = self.tardis_config.plasma.radiative_rates_type
         w_epsilon = self.tardis_config.plasma.w_epsilon
 
-        if radiative_rates_type == 'blackbody':
+        if radiative_rates_type == 'lte':
             logger.info('Calculating J_blues for radiative_rates_type=lte')
             j_blues = intensity_black_body(nus[np.newaxis].T, self.t_rads.value)
             self.j_blues = pd.DataFrame(j_blues, index=self.atom_data.lines.index, columns=np.arange(len(self.t_rads)))
@@ -200,11 +201,12 @@ def calculate_j_blues(self, init_detailed_j_blues=False):
 
     def update_plasmas(self, initialize_nlte=False):
 
-        self.plasma_array.update_radiationfield(self.t_rads.value, self.ws, self.j_blues,
-            self.tardis_config.plasma.nlte, initialize_nlte=initialize_nlte, n_e_convergence_threshold=0.05)
+        self.plasma_array.update_radiationfield(self.t_rads.value, self.ws, j_blues=self.j_blues,
+                                        initialize_nlte=initialize_nlte)
+
 
         if self.tardis_config.plasma.line_interaction_type in ('downbranch', 'macroatom'):
-            self.transition_probabilities = self.plasma_array.transition_probabilities
+            self.transition_probabilities = self.plasma_array.calculate_transition_probabilities()
 
 
     def update_radiationfield(self, log_sampling=5):
@@ -283,6 +285,7 @@ def update_radiationfield(self, log_sampling=5):
                     self.tardis_config.supernova.luminosity_requested.value)
         logger.info('Calculating new t_inner = %.3f', updated_t_inner.value)
 
+
         return t_inner_new