From b5854bc6cea01d67d398115f8a551b3cbd10f204 Mon Sep 17 00:00:00 2001
From: Fotis Tsamis <ftsamis@gmail.com>
Date: Tue, 26 Jul 2016 19:33:15 +0300
Subject: [PATCH 01/15] Change MontecarloRunner so it doesn't depend on a
 Configuration object.

---
 tardis/montecarlo/base.py | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/tardis/montecarlo/base.py b/tardis/montecarlo/base.py
index 9ce42a283e6..efa6df53da0 100644
--- a/tardis/montecarlo/base.py
+++ b/tardis/montecarlo/base.py
@@ -53,18 +53,18 @@ def _initialize_estimator_arrays(self, no_of_shells, tau_sobolev_shape):
         self.Edotlu_estimator = np.zeros(tau_sobolev_shape)
 
 
-    def _initialize_geometry_arrays(self, structure):
+    def _initialize_geometry_arrays(self, model):
         """
         Generate the cgs like geometry arrays for the montecarlo part
 
         Parameters
         ----------
 
-        structure: ~ConfigurationNameSpace
+        model : model.Radial1DModel
         """
-        self.r_inner_cgs = structure.r_inner.to('cm').value
-        self.r_outer_cgs = structure.r_outer.to('cm').value
-        self.v_inner_cgs = structure.v_inner.to('cm/s').value
+        self.r_inner_cgs = model.r_inner.to('cm').value
+        self.r_outer_cgs = model.r_outer.to('cm').value
+        self.v_inner_cgs = model.v_inner.to('cm/s').value
 
     def _initialize_packets(self, T, no_of_packets, no_of_virtual_packets=None):
         nus, mus, energies = self.packet_source.create_packets(T, no_of_packets)
@@ -123,10 +123,10 @@ def run(self, model, no_of_packets, no_of_virtual_packets=0, nthreads=1,last_run
         :return:
         """
         self.time_of_simulation = model.time_of_simulation
-        self.volume = model.tardis_config.structure.volumes
+        self.volume = model.volume
         self._initialize_estimator_arrays(self.volume.shape[0],
                                           model.plasma.tau_sobolevs.shape)
-        self._initialize_geometry_arrays(model.tardis_config.structure)
+        self._initialize_geometry_arrays(model)
 
         self._initialize_packets(model.t_inner.value,
                                  no_of_packets)

From 5f83ef539c5b1d94764cf1a75ae214e874e7bc1a Mon Sep 17 00:00:00 2001
From: Fotis Tsamis <ftsamis@gmail.com>
Date: Tue, 26 Jul 2016 19:41:31 +0300
Subject: [PATCH 02/15] Add a plasma parameter to MontecarloRunner.run

The MontecarloRunner now needs a separate reference to the plasma since the restructured Radial1DModel doesn't have the plasma as an attribute anymore.
---
 tardis/montecarlo/base.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/tardis/montecarlo/base.py b/tardis/montecarlo/base.py
index efa6df53da0..add7107e297 100644
--- a/tardis/montecarlo/base.py
+++ b/tardis/montecarlo/base.py
@@ -110,7 +110,7 @@ def legacy_update_spectrum(self, no_of_virtual_packets):
             self.spectrum_virtual.update_luminosity(
                 self.montecarlo_virtual_luminosity)
 
-    def run(self, model, no_of_packets, no_of_virtual_packets=0, nthreads=1,last_run=False):
+    def run(self, model, plasma, no_of_packets, no_of_virtual_packets=0, nthreads=1,last_run=False):
         """
         Running the TARDIS simulation
 
@@ -118,6 +118,7 @@ def run(self, model, no_of_packets, no_of_virtual_packets=0, nthreads=1,last_run
         ----------
 
         :param model:
+        :param plasma:
         :param no_of_virtual_packets:
         :param nthreads:
         :return:
@@ -125,7 +126,7 @@ def run(self, model, no_of_packets, no_of_virtual_packets=0, nthreads=1,last_run
         self.time_of_simulation = model.time_of_simulation
         self.volume = model.volume
         self._initialize_estimator_arrays(self.volume.shape[0],
-                                          model.plasma.tau_sobolevs.shape)
+                                          plasma.tau_sobolevs.shape)
         self._initialize_geometry_arrays(model)
 
         self._initialize_packets(model.t_inner.value,

From 9f4385ec00740cc52be07d5c48b7bd7ba47f08a8 Mon Sep 17 00:00:00 2001
From: Fotis Tsamis <ftsamis@gmail.com>
Date: Thu, 4 Aug 2016 02:54:40 +0300
Subject: [PATCH 03/15] Move and adapt calculate_j_blues from the old
 Radial1DModel to MontecarloRunner.

---
 tardis/montecarlo/base.py | 41 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 41 insertions(+)

diff --git a/tardis/montecarlo/base.py b/tardis/montecarlo/base.py
index add7107e297..5a095720aa2 100644
--- a/tardis/montecarlo/base.py
+++ b/tardis/montecarlo/base.py
@@ -8,6 +8,7 @@
 from spectrum import TARDISSpectrum
 
 from tardis.montecarlo import montecarlo, packet_source
+from tardis.util import intensity_black_body
 from tardis.io.util import to_hdf
 
 import numpy as np
@@ -284,6 +285,46 @@ def calculate_f_nu(self, frequency):
     def calculate_f_lambda(self, wavelength):
         pass
 
+    def calculate_j_blues(self, model, plasma, atom_data,
+                          init_detailed_j_blues=False):
+        nus = atom_data.lines.nu.values
+        radiative_rates_type = plasma.radiative_rates_type
+        w_epsilon = plasma.w_epsilon
+
+        if radiative_rates_type == 'blackbody':
+            logger.info('Calculating J_blues for radiative_rates_type=lte')
+            j_blues = intensity_black_body(nus[np.newaxis].T, model.t_rad.value)
+            return pd.DataFrame(
+                j_blues, index=atom_data.lines.index,
+                columns=np.arange(len(model.t_rad)))
+
+        elif radiative_rates_type == 'dilute-blackbody' or init_detailed_j_blues:
+            logger.info('Calculating J_blues for radiative_rates_type=dilute-blackbody')
+            j_blues = model.w * intensity_black_body(nus[np.newaxis].T, model.t_rad.value)
+            return pd.DataFrame(
+                j_blues, index=atom_data.lines.index,
+                columns=np.arange(len(model.t_rad)))
+
+        elif radiative_rates_type == 'detailed':
+            logger.info('Calculating J_blues for radiate_rates_type=detailed')
+            j_blues_norm_factor = (const.c.cgs * model.time_explosion /
+            (4 * np.pi * model.time_of_simulation * model.volume))
+            j_blues = pd.DataFrame(
+                self.j_blue_estimator *
+                    j_blues_norm_factor.value,
+                    index=atom_data.lines.index,
+                    columns=np.arange(len(model.t_rad)))
+
+            for i in xrange(model.no_of_shells):
+                zero_j_blues = j_blues[i] == 0.0
+                j_blues[i][zero_j_blues] = (
+                    w_epsilon * intensity_black_body(
+                        atom_data.lines.nu[zero_j_blues].values,
+                        model.t_rad.value[i]))
+
+        else:
+            raise ValueError('radiative_rates_type type unknown - %s', radiative_rates_type)
+
     def to_hdf(self, path_or_buf, path=''):
         """
         Store the runner to an HDF structure.

From fc8da950ee5b62a9be9d485027fa3bf44dcaaa88 Mon Sep 17 00:00:00 2001
From: Fotis Tsamis <ftsamis@gmail.com>
Date: Thu, 4 Aug 2016 17:20:31 +0300
Subject: [PATCH 04/15] Add the time_of_simulation property to the
 MontecarloRunner.

---
 tardis/montecarlo/base.py | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/tardis/montecarlo/base.py b/tardis/montecarlo/base.py
index 5a095720aa2..6d7ad3ee31a 100644
--- a/tardis/montecarlo/base.py
+++ b/tardis/montecarlo/base.py
@@ -124,7 +124,7 @@ def run(self, model, plasma, no_of_packets, no_of_virtual_packets=0, nthreads=1,
         :param nthreads:
         :return:
         """
-        self.time_of_simulation = model.time_of_simulation
+        self.time_of_simulation = self.calculate_time_of_simulation(model)
         self.volume = model.volume
         self._initialize_estimator_arrays(self.volume.shape[0],
                                           plasma.tau_sobolevs.shape)
@@ -325,6 +325,13 @@ def calculate_j_blues(self, model, plasma, atom_data,
         else:
             raise ValueError('radiative_rates_type type unknown - %s', radiative_rates_type)
 
+    def calculate_time_of_simulation(self, model):
+        luminosity_inner = (
+            4 * np.pi * const.sigma_sb.cgs * model.r_inner[0] ** 2 *
+            model.t_inner ** 4).to('erg/s')
+
+        return 1.0 * u.erg / luminosity_inner
+
     def to_hdf(self, path_or_buf, path=''):
         """
         Store the runner to an HDF structure.

From f777f8fe33ea3c5e712bc6861d111d8c4016b2ea Mon Sep 17 00:00:00 2001
From: Fotis Tsamis <ftsamis@gmail.com>
Date: Fri, 5 Aug 2016 22:33:12 +0300
Subject: [PATCH 05/15] Add the plasma as an argument to
 montecarlo.montecarlo_radial1d.

---
 tardis/montecarlo/base.py        |  2 +-
 tardis/montecarlo/montecarlo.pyx | 18 +++++++++---------
 2 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/tardis/montecarlo/base.py b/tardis/montecarlo/base.py
index 6d7ad3ee31a..e661d9feb4b 100644
--- a/tardis/montecarlo/base.py
+++ b/tardis/montecarlo/base.py
@@ -134,7 +134,7 @@ def run(self, model, plasma, no_of_packets, no_of_virtual_packets=0, nthreads=1,
                                  no_of_packets)
 
         montecarlo.montecarlo_radial1d(
-            model, self, virtual_packet_flag=no_of_virtual_packets,
+            model, plasma, self, virtual_packet_flag=no_of_virtual_packets,
             nthreads=nthreads,last_run=last_run)
         # Workaround so that j_blue_estimator is in the right ordering
         # They are written as an array of dimension (no_of_shells, no_of_lines)
diff --git a/tardis/montecarlo/montecarlo.pyx b/tardis/montecarlo/montecarlo.pyx
index 8e412fde4b3..29244ee4748 100644
--- a/tardis/montecarlo/montecarlo.pyx
+++ b/tardis/montecarlo/montecarlo.pyx
@@ -93,7 +93,7 @@ cdef extern from "src/cmontecarlo.h":
 
 
 
-cdef initialize_storage_model(model, runner, storage_model_t *storage):
+cdef initialize_storage_model(model, plasma, runner, storage_model_t *storage):
     """
     Initializing the storage struct.
 
@@ -120,10 +120,10 @@ cdef initialize_storage_model(model, runner, storage_model_t *storage):
     storage.inverse_time_explosion = 1.0 / storage.time_explosion
     #electron density
     storage.electron_densities = <double*> PyArray_DATA(
-        model.plasma.electron_densities.values)
+        plasma.electron_densities.values)
 
     runner.inverse_electron_densities = (
-        1.0 / model.plasma.electron_densities.values)
+        1.0 / plasma.electron_densities.values)
     storage.inverse_electron_densities = <double*> PyArray_DATA(
         runner.inverse_electron_densities)
     # Switch for continuum processes
@@ -149,7 +149,7 @@ cdef initialize_storage_model(model, runner, storage_model_t *storage):
     storage.no_of_lines = model.atom_data.lines.nu.values.size
     storage.line_list_nu = <double*> PyArray_DATA(model.atom_data.lines.nu.values)
     runner.line_lists_tau_sobolevs = (
-            model.plasma.tau_sobolevs.values.flatten(order='F')
+            plasma.tau_sobolevs.values.flatten(order='F')
             )
     storage.line_lists_tau_sobolevs = <double*> PyArray_DATA(
             runner.line_lists_tau_sobolevs
@@ -166,13 +166,13 @@ cdef initialize_storage_model(model, runner, storage_model_t *storage):
     # macro atom & downbranch
     if storage.line_interaction_id >= 1:
         runner.transition_probabilities = (
-                model.plasma.transition_probabilities.values.flatten(order='F')
+                plasma.transition_probabilities.values.flatten(order='F')
         )
         storage.transition_probabilities = <double*> PyArray_DATA(
                 runner.transition_probabilities
                 )
         storage.transition_probabilities_nd = (
-        model.plasma.transition_probabilities.values.shape[0])
+        plasma.transition_probabilities.values.shape[0])
         storage.line2macro_level_upper = <int_type_t*> PyArray_DATA(
             model.atom_data.lines_upper2macro_reference_idx)
         storage.macro_block_references = <int_type_t*> PyArray_DATA(
@@ -218,10 +218,10 @@ cdef initialize_storage_model(model, runner, storage_model_t *storage):
     storage.reflective_inner_boundary = model.tardis_config.montecarlo.enable_reflective_inner_boundary
     storage.inner_boundary_albedo = model.tardis_config.montecarlo.inner_boundary_albedo
     # Data for continuum implementation
-    cdef np.ndarray[double, ndim=1] t_electrons = model.plasma.t_electrons
+    cdef np.ndarray[double, ndim=1] t_electrons = plasma.t_electrons
     storage.t_electrons = <double*> t_electrons.data
 
-def montecarlo_radial1d(model, runner, int_type_t virtual_packet_flag=0,
+def montecarlo_radial1d(model, plasma, runner, int_type_t virtual_packet_flag=0,
                         int nthreads=4,last_run=False):
     """
     Parameters
@@ -253,7 +253,7 @@ def montecarlo_radial1d(model, runner, int_type_t virtual_packet_flag=0,
 
     cdef storage_model_t storage
 
-    initialize_storage_model(model, runner, &storage)
+    initialize_storage_model(model, plasma, runner, &storage)
 
     montecarlo_main_loop(&storage, virtual_packet_flag, nthreads,
                          model.tardis_config.montecarlo.seed)

From 097454c1677af9da941f00da61ff4fa809404e26 Mon Sep 17 00:00:00 2001
From: Fotis Tsamis <ftsamis@gmail.com>
Date: Fri, 5 Aug 2016 22:39:47 +0300
Subject: [PATCH 06/15] Remove every Configuration object usage from the
 montecarlo.pyx

---
 tardis/montecarlo/base.py        | 11 ++++++++++-
 tardis/montecarlo/montecarlo.pyx | 33 +++++++++++++++-----------------
 2 files changed, 25 insertions(+), 19 deletions(-)

diff --git a/tardis/montecarlo/base.py b/tardis/montecarlo/base.py
index e661d9feb4b..ea85dd6bddd 100644
--- a/tardis/montecarlo/base.py
+++ b/tardis/montecarlo/base.py
@@ -29,9 +29,18 @@ class MontecarloRunner(object):
     t_rad_estimator_constant = ((np.pi**4 / (15 * 24 * zeta(5, 1))) *
                                 (const.h / const.k_B)).cgs.value
 
-    def __init__(self, seed, spectrum_frequency, distance=None):
+    def __init__(self, seed, spectrum_frequency, virtual_spectrum_range,
+                 sigma_thomson, enable_reflective_inner_boundary,
+                 inner_boundary_albedo, line_interaction_type, distance=None):
+
+        self.seed = seed
         self.packet_source = packet_source.BlackBodySimpleSource(seed)
         self.spectrum_frequency = spectrum_frequency
+        self.virtual_spectrum_range = virtual_spectrum_range # TODO: linspace handling
+        self.sigma_thomson = sigma_thomson
+        self.enable_reflective_inner_boundary = enable_reflective_inner_boundary
+        self.inner_boundary_albedo = inner_boundary_albedo
+        self.line_interaction_type = line_interaction_type
         self.spectrum = TARDISSpectrum(spectrum_frequency, distance)
         self.spectrum_virtual = TARDISSpectrum(spectrum_frequency, distance)
         self.spectrum_reabsorbed = TARDISSpectrum(spectrum_frequency, distance)
diff --git a/tardis/montecarlo/montecarlo.pyx b/tardis/montecarlo/montecarlo.pyx
index 29244ee4748..d58b0548554 100644
--- a/tardis/montecarlo/montecarlo.pyx
+++ b/tardis/montecarlo/montecarlo.pyx
@@ -105,8 +105,7 @@ cdef initialize_storage_model(model, plasma, runner, storage_model_t *storage):
     storage.packet_energies = <double*> PyArray_DATA(runner.input_energy)
 
     # Setup of structure
-    structure = model.tardis_config.structure
-    storage.no_of_shells = structure.no_of_shells
+    storage.no_of_shells = model.no_of_shells
 
 
     storage.r_inner = <double*> PyArray_DATA(runner.r_inner_cgs)
@@ -115,8 +114,7 @@ cdef initialize_storage_model(model, plasma, runner, storage_model_t *storage):
 
     # Setup the rest
     # times
-    storage.time_explosion = model.tardis_config.supernova.time_explosion.to(
-        's').value
+    storage.time_explosion = model.time_explosion.to('s').value
     storage.inverse_time_explosion = 1.0 / storage.time_explosion
     #electron density
     storage.electron_densities = <double*> PyArray_DATA(
@@ -161,7 +159,7 @@ cdef initialize_storage_model(model, plasma, runner, storage_model_t *storage):
             runner.Edotlu_estimator)
 
     storage.line_interaction_id = runner.get_line_interaction_id(
-        model.tardis_config.plasma.line_interaction_type)
+        runner.line_interaction_type)
 
     # macro atom & downbranch
     if storage.line_interaction_id >= 1:
@@ -203,20 +201,20 @@ cdef initialize_storage_model(model, plasma, runner, storage_model_t *storage):
     storage.js = <double*> PyArray_DATA(runner.j_estimator)
     storage.nubars = <double*> PyArray_DATA(runner.nu_bar_estimator)
 
-    storage.spectrum_start_nu = model.tardis_config.spectrum.frequency.value.min()
-    storage.spectrum_end_nu = model.tardis_config.spectrum.frequency.value.max()
-    storage.spectrum_virt_start_nu = model.tardis_config.montecarlo.virtual_spectrum_range.end.to('Hz', units.spectral()).value
-    storage.spectrum_virt_end_nu = model.tardis_config.montecarlo.virtual_spectrum_range.start.to('Hz', units.spectral()).value
-    storage.spectrum_delta_nu = model.tardis_config.spectrum.frequency.value[1] - model.tardis_config.spectrum.frequency.value[0]
+    storage.spectrum_start_nu = runner.spectrum_frequency.value.min()
+    storage.spectrum_end_nu = runner.spectrum_frequency.value.max()
+    # TODO: Linspace handling for virtual_spectrum_range
+    storage.spectrum_virt_start_nu = runner.virtual_spectrum_range.end.to('Hz', units.spectral()).value
+    storage.spectrum_virt_end_nu = runner.virtual_spectrum_range.start.to('Hz', units.spectral()).value
+    storage.spectrum_delta_nu = runner.spectrum_frequency.value[1] - runner.spectrum_frequency.value[0]
 
     storage.spectrum_virt_nu = <double*> PyArray_DATA(
         runner.legacy_montecarlo_virtual_luminosity)
 
-    storage.sigma_thomson = (
-        model.tardis_config.montecarlo.sigma_thomson.cgs.value)
+    storage.sigma_thomson = runner.sigma_thomson.cgs.value
     storage.inverse_sigma_thomson = 1.0 / storage.sigma_thomson
-    storage.reflective_inner_boundary = model.tardis_config.montecarlo.enable_reflective_inner_boundary
-    storage.inner_boundary_albedo = model.tardis_config.montecarlo.inner_boundary_albedo
+    storage.reflective_inner_boundary = runner.enable_reflective_inner_boundary
+    storage.inner_boundary_albedo = runner.inner_boundary_albedo
     # Data for continuum implementation
     cdef np.ndarray[double, ndim=1] t_electrons = plasma.t_electrons
     storage.t_electrons = <double*> t_electrons.data
@@ -255,8 +253,7 @@ def montecarlo_radial1d(model, plasma, runner, int_type_t virtual_packet_flag=0,
 
     initialize_storage_model(model, plasma, runner, &storage)
 
-    montecarlo_main_loop(&storage, virtual_packet_flag, nthreads,
-                         model.tardis_config.montecarlo.seed)
+    montecarlo_main_loop(&storage, virtual_packet_flag, nthreads, runner.seed)
     cdef np.ndarray[double, ndim=1] virt_packet_nus = np.zeros(storage.virt_packet_count, dtype=np.float64)
     cdef np.ndarray[double, ndim=1] virt_packet_energies = np.zeros(storage.virt_packet_count, dtype=np.float64)
     cdef np.ndarray[double, ndim=1] virt_packet_last_interaction_in_nu = np.zeros(storage.virt_packet_count, dtype=np.float64)
@@ -298,8 +295,8 @@ def montecarlo_radial1d(model, plasma, runner, int_type_t virtual_packet_flag=0,
 
 def postprocess(model, runner):
     Edotlu_norm_factor = (1 /
-        (model.time_of_simulation * model.tardis_config.structure.volumes))
+        (runner.time_of_simulation * model.volume))
     exptau = 1 - np.exp(-
                         runner.line_lists_tau_sobolevs.reshape(-1,
                             runner.j_estimator.shape[0]) )
-    model.Edotlu = Edotlu_norm_factor*exptau*runner.Edotlu_estimator
+    runner.Edotlu = Edotlu_norm_factor*exptau*runner.Edotlu_estimator

From 894510cd9fe8288983e3b54a549a43fd92b7d400 Mon Sep 17 00:00:00 2001
From: Fotis Tsamis <ftsamis@gmail.com>
Date: Fri, 5 Aug 2016 22:47:44 +0300
Subject: [PATCH 07/15] Add a from_config classmethod to the MontecarloRunner.

---
 tardis/montecarlo/base.py | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/tardis/montecarlo/base.py b/tardis/montecarlo/base.py
index ea85dd6bddd..13960f61b9d 100644
--- a/tardis/montecarlo/base.py
+++ b/tardis/montecarlo/base.py
@@ -366,3 +366,14 @@ def to_hdf(self, path_or_buf, path=''):
                                      'spectrum_virtual')
         self.spectrum_reabsorbed.to_hdf(path_or_buf, runner_path,
                                         'spectrum_reabsorbed')
+
+    @classmethod
+    def from_config(cls, config):
+        return cls(seed=config.montecarlo.seed,
+                   spectrum_frequency=config.spectrum.frequency,
+                   virtual_spectrum_range=config.montecarlo.virtual_spectrum_range,
+                   sigma_thomson=config.montecarlo.sigma_thomson,
+                   enable_reflective_inner_boundary=config.montecarlo.enable_reflective_inner_boundary,
+                   inner_boundary_albedo=config.montecarlo.inner_boundary_albedo,
+                   line_interaction_type=config.plasma.line_interaction_type,
+                   distance=config.supernova.get('distance', None))
\ No newline at end of file

From f69c995df8e1827fcd5b46a4c8f91a4bf36c3f56 Mon Sep 17 00:00:00 2001
From: Fotis Tsamis <ftsamis@gmail.com>
Date: Mon, 8 Aug 2016 13:30:08 +0300
Subject: [PATCH 08/15] montecarlo.pyx: Access atomic_data from the plasma,
 instead of model.

---
 tardis/montecarlo/montecarlo.pyx | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/tardis/montecarlo/montecarlo.pyx b/tardis/montecarlo/montecarlo.pyx
index d58b0548554..682e3c8859f 100644
--- a/tardis/montecarlo/montecarlo.pyx
+++ b/tardis/montecarlo/montecarlo.pyx
@@ -144,8 +144,8 @@ cdef initialize_storage_model(model, plasma, runner, storage_model_t *storage):
         storage.l_pop_r = <double*> l_pop_r.data
 
     # Line lists
-    storage.no_of_lines = model.atom_data.lines.nu.values.size
-    storage.line_list_nu = <double*> PyArray_DATA(model.atom_data.lines.nu.values)
+    storage.no_of_lines = plasma.atomic_data.lines.nu.values.size
+    storage.line_list_nu = <double*> PyArray_DATA(plasma.atomic_data.lines.nu.values)
     runner.line_lists_tau_sobolevs = (
             plasma.tau_sobolevs.values.flatten(order='F')
             )
@@ -172,17 +172,17 @@ cdef initialize_storage_model(model, plasma, runner, storage_model_t *storage):
         storage.transition_probabilities_nd = (
         plasma.transition_probabilities.values.shape[0])
         storage.line2macro_level_upper = <int_type_t*> PyArray_DATA(
-            model.atom_data.lines_upper2macro_reference_idx)
+            plasma.atomic_data.lines_upper2macro_reference_idx)
         storage.macro_block_references = <int_type_t*> PyArray_DATA(
-            model.atom_data.macro_atom_references['block_references'].values)
+            plasma.atomic_data.macro_atom_references['block_references'].values)
         storage.transition_type = <int_type_t*> PyArray_DATA(
-            model.atom_data.macro_atom_data['transition_type'].values)
+            plasma.atomic_data.macro_atom_data['transition_type'].values)
 
         # Destination level is not needed and/or generated for downbranch
         storage.destination_level_id = <int_type_t*> PyArray_DATA(
-            model.atom_data.macro_atom_data['destination_level_idx'].values)
+            plasma.atomic_data.macro_atom_data['destination_level_idx'].values)
         storage.transition_line_id = <int_type_t*> PyArray_DATA(
-            model.atom_data.macro_atom_data['lines_idx'].values)
+            plasma.atomic_data.macro_atom_data['lines_idx'].values)
 
     storage.output_nus = <double*> PyArray_DATA(runner._output_nu)
     storage.output_energies = <double*> PyArray_DATA(runner._output_energy)

From 0e7cf7dbe97432d1ce28cf76aa7a742961050ff3 Mon Sep 17 00:00:00 2001
From: Fotis Tsamis <ftsamis@gmail.com>
Date: Tue, 9 Aug 2016 19:24:53 +0300
Subject: [PATCH 09/15] Revert "Move and adapt calculate_j_blues from the old
 Radial1DModel to MontecarloRunner."

This reverts commit 9f4385ec00740cc52be07d5c48b7bd7ba47f08a8, because it
was decided that the j_blues will become plasma properties.
---
 tardis/montecarlo/base.py | 48 ---------------------------------------
 1 file changed, 48 deletions(-)

diff --git a/tardis/montecarlo/base.py b/tardis/montecarlo/base.py
index 13960f61b9d..6be054e55ce 100644
--- a/tardis/montecarlo/base.py
+++ b/tardis/montecarlo/base.py
@@ -8,7 +8,6 @@
 from spectrum import TARDISSpectrum
 
 from tardis.montecarlo import montecarlo, packet_source
-from tardis.util import intensity_black_body
 from tardis.io.util import to_hdf
 
 import numpy as np
@@ -294,53 +293,6 @@ def calculate_f_nu(self, frequency):
     def calculate_f_lambda(self, wavelength):
         pass
 
-    def calculate_j_blues(self, model, plasma, atom_data,
-                          init_detailed_j_blues=False):
-        nus = atom_data.lines.nu.values
-        radiative_rates_type = plasma.radiative_rates_type
-        w_epsilon = plasma.w_epsilon
-
-        if radiative_rates_type == 'blackbody':
-            logger.info('Calculating J_blues for radiative_rates_type=lte')
-            j_blues = intensity_black_body(nus[np.newaxis].T, model.t_rad.value)
-            return pd.DataFrame(
-                j_blues, index=atom_data.lines.index,
-                columns=np.arange(len(model.t_rad)))
-
-        elif radiative_rates_type == 'dilute-blackbody' or init_detailed_j_blues:
-            logger.info('Calculating J_blues for radiative_rates_type=dilute-blackbody')
-            j_blues = model.w * intensity_black_body(nus[np.newaxis].T, model.t_rad.value)
-            return pd.DataFrame(
-                j_blues, index=atom_data.lines.index,
-                columns=np.arange(len(model.t_rad)))
-
-        elif radiative_rates_type == 'detailed':
-            logger.info('Calculating J_blues for radiate_rates_type=detailed')
-            j_blues_norm_factor = (const.c.cgs * model.time_explosion /
-            (4 * np.pi * model.time_of_simulation * model.volume))
-            j_blues = pd.DataFrame(
-                self.j_blue_estimator *
-                    j_blues_norm_factor.value,
-                    index=atom_data.lines.index,
-                    columns=np.arange(len(model.t_rad)))
-
-            for i in xrange(model.no_of_shells):
-                zero_j_blues = j_blues[i] == 0.0
-                j_blues[i][zero_j_blues] = (
-                    w_epsilon * intensity_black_body(
-                        atom_data.lines.nu[zero_j_blues].values,
-                        model.t_rad.value[i]))
-
-        else:
-            raise ValueError('radiative_rates_type type unknown - %s', radiative_rates_type)
-
-    def calculate_time_of_simulation(self, model):
-        luminosity_inner = (
-            4 * np.pi * const.sigma_sb.cgs * model.r_inner[0] ** 2 *
-            model.t_inner ** 4).to('erg/s')
-
-        return 1.0 * u.erg / luminosity_inner
-
     def to_hdf(self, path_or_buf, path=''):
         """
         Store the runner to an HDF structure.

From f410a6073783bab145508435dc1364c8eb3c0329 Mon Sep 17 00:00:00 2001
From: Fotis Tsamis <ftsamis@gmail.com>
Date: Tue, 9 Aug 2016 22:48:55 +0300
Subject: [PATCH 10/15] Add a calculate_time_of_simulation and a
 calculate_luminosity_inner to the MontecarloRunner.

---
 tardis/montecarlo/base.py | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/tardis/montecarlo/base.py b/tardis/montecarlo/base.py
index 6be054e55ce..2e312a2a9c9 100644
--- a/tardis/montecarlo/base.py
+++ b/tardis/montecarlo/base.py
@@ -287,6 +287,13 @@ def calculate_radiationfield_properties(self):
 
         return t_rad * u.K, w
 
+    def calculate_luminosity_inner(self, model):
+        return (4 * np.pi * const.sigma_sb.cgs *
+                model.r_inner[0] ** 2 * model.t_inner ** 4).to('erg/s')
+
+    def calculate_time_of_simulation(self, model):
+        return (1.0 * u.erg / self.calculate_luminosity_inner(model))
+
     def calculate_f_nu(self, frequency):
         pass
 

From 3895e14e20fa1d1ba28e4bc53f74773f2ca771d1 Mon Sep 17 00:00:00 2001
From: Fotis Tsamis <ftsamis@gmail.com>
Date: Sun, 14 Aug 2016 00:13:26 +0300
Subject: [PATCH 11/15] Move the sigma_thomson calculation from config_reader
 to montecarlo.

---
 tardis/io/config_reader.py | 16 ----------------
 tardis/montecarlo/base.py  | 10 +++++++++-
 2 files changed, 9 insertions(+), 17 deletions(-)

diff --git a/tardis/io/config_reader.py b/tardis/io/config_reader.py
index 6fc603d5e9f..960ff5ce5d3 100644
--- a/tardis/io/config_reader.py
+++ b/tardis/io/config_reader.py
@@ -943,22 +943,6 @@ def from_config_dict(cls, config_dict, atom_data=None, test_parser=False,
         else:
             plasma_section['t_rads'] = None
 
-        if plasma_section['disable_electron_scattering'] is False:
-            logger.debug("Electron scattering switched on")
-            validated_config_dict['montecarlo']['sigma_thomson'] = 6.652486e-25 / (u.cm ** 2)
-        else:
-            logger.warn('Disabling electron scattering - this is not physical')
-            validated_config_dict['montecarlo']['sigma_thomson'] = 1e-200 / (u.cm ** 2)
-
-        if plasma_section['helium_treatment'] == 'recomb-nlte':
-            validated_config_dict['plasma']['helium_treatment'] == 'recomb-nlte'
-        else:
-            validated_config_dict['plasma']['helium_treatment'] == 'dilute-lte'
-
-
-
-
-
         ##### NLTE subsection of Plasma start
         nlte_validated_config_dict = {}
         nlte_species = []
diff --git a/tardis/montecarlo/base.py b/tardis/montecarlo/base.py
index 2e312a2a9c9..279eb36f721 100644
--- a/tardis/montecarlo/base.py
+++ b/tardis/montecarlo/base.py
@@ -328,10 +328,18 @@ def to_hdf(self, path_or_buf, path=''):
 
     @classmethod
     def from_config(cls, config):
+        if config.plasma.disable_electron_scattering:
+            logger.warn('Disabling electron scattering - this is not physical')
+            sigma_thomson = 1e-200 / (u.cm ** 2)
+        else:
+            logger.debug("Electron scattering switched on")
+            sigma_thomson = 6.652486e-25 / (u.cm ** 2)
+
+
         return cls(seed=config.montecarlo.seed,
                    spectrum_frequency=config.spectrum.frequency,
                    virtual_spectrum_range=config.montecarlo.virtual_spectrum_range,
-                   sigma_thomson=config.montecarlo.sigma_thomson,
+                   sigma_thomson=sigma_thomson,
                    enable_reflective_inner_boundary=config.montecarlo.enable_reflective_inner_boundary,
                    inner_boundary_albedo=config.montecarlo.inner_boundary_albedo,
                    line_interaction_type=config.plasma.line_interaction_type,

From 52071c8b2e163c7f8f14e968b7ec16ea072c7439 Mon Sep 17 00:00:00 2001
From: Fotis Tsamis <ftsamis@gmail.com>
Date: Sun, 14 Aug 2016 00:22:14 +0300
Subject: [PATCH 12/15] Move the spectrum frequency calculation from
 config_reader to montecarlo.

---
 tardis/io/config_reader.py            | 33 ---------------------------
 tardis/io/tests/test_config_reader.py |  8 -------
 tardis/montecarlo/base.py             |  8 +++++--
 3 files changed, 6 insertions(+), 43 deletions(-)

diff --git a/tardis/io/config_reader.py b/tardis/io/config_reader.py
index 960ff5ce5d3..c7f2aaf9fcf 100644
--- a/tardis/io/config_reader.py
+++ b/tardis/io/config_reader.py
@@ -480,35 +480,6 @@ def parse_supernova_section(supernova_dict):
     return config_dict
 
 
-def parse_spectrum_list2dict(spectrum_list):
-    """
-    Parse the spectrum list [start, stop, num] to a list
-    """
-    if 'start' in spectrum_list and 'stop' in spectrum_list \
-            and 'num' in spectrum_list:
-        spectrum_list = [spectrum_list['start'], spectrum_list['stop'],
-                         spectrum_list['num']]
-    if spectrum_list[0].unit.physical_type != 'length' and \
-                    spectrum_list[1].unit.physical_type != 'length':
-        raise ValueError('start and end of spectrum need to be a length')
-
-
-    spectrum_config_dict = {}
-    spectrum_config_dict['start'] = spectrum_list[0]
-    spectrum_config_dict['end'] = spectrum_list[1]
-    spectrum_config_dict['bins'] = spectrum_list[2]
-
-    spectrum_frequency = quantity_linspace(
-        spectrum_config_dict['end'].to('Hz', u.spectral()),
-        spectrum_config_dict['start'].to('Hz', u.spectral()),
-        num=spectrum_config_dict['bins'] + 1)
-
-    spectrum_config_dict['frequency'] = spectrum_frequency
-
-    return spectrum_config_dict
-
-
-
 def parse_convergence_section(convergence_section_dict):
     """
     Parse the convergence section dictionary
@@ -1010,10 +981,6 @@ def from_config_dict(cls, config_dict, atom_data=None, test_parser=False,
 
         ###### END of convergence section reading
 
-
-        validated_config_dict['spectrum'] = parse_spectrum_list2dict(
-            validated_config_dict['spectrum'])
-
         return cls(validated_config_dict, atom_data)
 
 
diff --git a/tardis/io/tests/test_config_reader.py b/tardis/io/tests/test_config_reader.py
index 073f8b39a68..56aafe9ddbf 100644
--- a/tardis/io/tests/test_config_reader.py
+++ b/tardis/io/tests/test_config_reader.py
@@ -31,14 +31,6 @@ def test_quantity_linspace():
     assert len(quantity_linspace) == 1000
 
 
-def test_spectrum_list2_dict():
-    spectrum_dict = config_reader.parse_spectrum_list2dict(
-        [200*u.angstrom, 10000 * u.angstrom, 100])
-    assert_almost_equal(spectrum_dict['start'].to(u.angstrom).value, 200)
-    assert_almost_equal(spectrum_dict['end'].to(u.angstrom).value, 10000)
-    assert_almost_equal(spectrum_dict['bins'], 100)
-
-
 def test_convergence_section_parser():
     test_convergence_section = {'type': 'damped',
                                 'lock_t_inner_cyles': 1,
diff --git a/tardis/montecarlo/base.py b/tardis/montecarlo/base.py
index 279eb36f721..feda90244f3 100644
--- a/tardis/montecarlo/base.py
+++ b/tardis/montecarlo/base.py
@@ -7,6 +7,7 @@
 from scipy.special import zeta
 from spectrum import TARDISSpectrum
 
+from tardis.util import quantity_linspace
 from tardis.montecarlo import montecarlo, packet_source
 from tardis.io.util import to_hdf
 
@@ -335,9 +336,12 @@ def from_config(cls, config):
             logger.debug("Electron scattering switched on")
             sigma_thomson = 6.652486e-25 / (u.cm ** 2)
 
-
+        spectrum_frequency = quantity_linspace(
+            config.spectrum.stop.to('Hz', u.spectral()),
+            config.spectrum.start.to('Hz', u.spectral()),
+            num=config.spectrum.num + 1)
         return cls(seed=config.montecarlo.seed,
-                   spectrum_frequency=config.spectrum.frequency,
+                   spectrum_frequency=spectrum_frequency,
                    virtual_spectrum_range=config.montecarlo.virtual_spectrum_range,
                    sigma_thomson=sigma_thomson,
                    enable_reflective_inner_boundary=config.montecarlo.enable_reflective_inner_boundary,

From 790737ca92ce178b3f54bf91233aee513ad18a7c Mon Sep 17 00:00:00 2001
From: Fotis Tsamis <ftsamis@gmail.com>
Date: Sun, 14 Aug 2016 00:50:26 +0300
Subject: [PATCH 13/15] Remove supernova distance checking from config_dict

---
 tardis/io/config_reader.py | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/tardis/io/config_reader.py b/tardis/io/config_reader.py
index c7f2aaf9fcf..ca958c77e54 100644
--- a/tardis/io/config_reader.py
+++ b/tardis/io/config_reader.py
@@ -460,11 +460,6 @@ def parse_supernova_section(supernova_dict):
 
     config_dict['time_explosion'] = parse_quantity(supernova_dict['time_explosion']).to('s')
 
-    if 'distance' in supernova_dict:
-        config_dict['distance'] = parse_quantity(supernova_dict['distance'])
-    else:
-        config_dict['distance'] = None
-
     if 'luminosity_wavelength_start' in supernova_dict:
         config_dict['luminosity_nu_end'] = parse_quantity(supernova_dict['luminosity_wavelength_start']). \
             to('Hz', u.spectral())

From 931751efa5bc0462822767a61fe7378c6d0936bc Mon Sep 17 00:00:00 2001
From: Fotis Tsamis <ftsamis@gmail.com>
Date: Sun, 14 Aug 2016 01:06:23 +0300
Subject: [PATCH 14/15] Don't rename virtual_spectrum_range's stop and num to
 end and samples.

---
 tardis/io/config_reader.py       | 8 --------
 tardis/montecarlo/base.py        | 2 ++
 tardis/montecarlo/montecarlo.pyx | 2 +-
 3 files changed, 3 insertions(+), 9 deletions(-)

diff --git a/tardis/io/config_reader.py b/tardis/io/config_reader.py
index ca958c77e54..77a72d6c32d 100644
--- a/tardis/io/config_reader.py
+++ b/tardis/io/config_reader.py
@@ -965,14 +965,6 @@ def from_config_dict(cls, config_dict, atom_data=None, test_parser=False,
             black_body_section['stop']
         montecarlo_section['black_body_sampling']['samples'] = \
             black_body_section['num']
-        virtual_spectrum_section = montecarlo_section['virtual_spectrum_range']
-        montecarlo_section['virtual_spectrum_range'] = {}
-        montecarlo_section['virtual_spectrum_range']['start'] = \
-            virtual_spectrum_section['start']
-        montecarlo_section['virtual_spectrum_range']['end'] = \
-            virtual_spectrum_section['stop']
-        montecarlo_section['virtual_spectrum_range']['samples'] = \
-            virtual_spectrum_section['num']
 
         ###### END of convergence section reading
 
diff --git a/tardis/montecarlo/base.py b/tardis/montecarlo/base.py
index feda90244f3..00fbcd6867e 100644
--- a/tardis/montecarlo/base.py
+++ b/tardis/montecarlo/base.py
@@ -340,8 +340,10 @@ def from_config(cls, config):
             config.spectrum.stop.to('Hz', u.spectral()),
             config.spectrum.start.to('Hz', u.spectral()),
             num=config.spectrum.num + 1)
+
         return cls(seed=config.montecarlo.seed,
                    spectrum_frequency=spectrum_frequency,
+                   # TODO: Linspace handling for virtual_spectrum_range
                    virtual_spectrum_range=config.montecarlo.virtual_spectrum_range,
                    sigma_thomson=sigma_thomson,
                    enable_reflective_inner_boundary=config.montecarlo.enable_reflective_inner_boundary,
diff --git a/tardis/montecarlo/montecarlo.pyx b/tardis/montecarlo/montecarlo.pyx
index 682e3c8859f..82f060b6af5 100644
--- a/tardis/montecarlo/montecarlo.pyx
+++ b/tardis/montecarlo/montecarlo.pyx
@@ -204,7 +204,7 @@ cdef initialize_storage_model(model, plasma, runner, storage_model_t *storage):
     storage.spectrum_start_nu = runner.spectrum_frequency.value.min()
     storage.spectrum_end_nu = runner.spectrum_frequency.value.max()
     # TODO: Linspace handling for virtual_spectrum_range
-    storage.spectrum_virt_start_nu = runner.virtual_spectrum_range.end.to('Hz', units.spectral()).value
+    storage.spectrum_virt_start_nu = runner.virtual_spectrum_range.stop.to('Hz', units.spectral()).value
     storage.spectrum_virt_end_nu = runner.virtual_spectrum_range.start.to('Hz', units.spectral()).value
     storage.spectrum_delta_nu = runner.spectrum_frequency.value[1] - runner.spectrum_frequency.value[0]
 

From dde78a86d4b97e65a1faa4efad608ce65133c010 Mon Sep 17 00:00:00 2001
From: Fotis Tsamis <ftsamis@gmail.com>
Date: Tue, 16 Aug 2016 22:33:42 +0300
Subject: [PATCH 15/15] Fix a bug when initializing the logger for
 montecarlo/base.py

---
 tardis/montecarlo/base.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tardis/montecarlo/base.py b/tardis/montecarlo/base.py
index 00fbcd6867e..c870834672c 100644
--- a/tardis/montecarlo/base.py
+++ b/tardis/montecarlo/base.py
@@ -14,7 +14,7 @@
 import numpy as np
 import pandas as pd
 
-logger = logging.getLevelName(__name__)
+logger = logging.getLogger(__name__)
 
 class MontecarloRunner(object):
     """