Feature request: add virtual-packet-logging option to run_tardis()

tardis/base.py

@@ -2,7 +2,11 @@
 
 
 def run_tardis(
-    config, atom_data=None, packet_source=None, simulation_callbacks=[]
+    config,
+    atom_data=None,
+    packet_source=None,
+    simulation_callbacks=[],
+    virtual_packet_logging=False,
 ):
     """
     This function is one of the core functions to run TARDIS from a given
@@ -19,6 +23,13 @@ def run_tardis(
         the atomic data. Atomic data to use for this TARDIS simulation. If set to None, the
         atomic data will be loaded according to keywords set in the configuration
         [default=None]
+    virtual_packet_logging : bool
+        option to enable virtual packet logging
+        [default=False]
+
+    Returns
+    -------
+    Simulation
     """
     from tardis.io.config_reader import Configuration
     from tardis.io.atom_data.base import AtomData
@@ -36,7 +47,10 @@ def run_tardis(
         tardis_config = Configuration.from_config_dict(config)
 
     simulation = Simulation.from_config(
-        tardis_config, packet_source=packet_source, atom_data=atom_data
+        tardis_config,
+        packet_source=packet_source,
+        atom_data=atom_data,
+        virtual_packet_logging=virtual_packet_logging,
     )
     for cb in simulation_callbacks:
         simulation.add_callback(*cb)

tardis/montecarlo/base.py

@@ -425,7 +425,18 @@ def montecarlo_virtual_luminosity(self):
     def calculate_emitted_luminosity(
         self, luminosity_nu_start, luminosity_nu_end
     ):
+        """
+        Calculate emitted luminosity.
+
+        Parameters
+        ----------
+        luminosity_nu_start : astropy.units.Quantity
+        luminosity_nu_end : astropy.units.Quantity
 
+        Returns
+        -------
+        astropy.units.Quantity
+        """
         luminosity_wavelength_filter = (
             self.emitted_packet_nu > luminosity_nu_start
         ) & (self.emitted_packet_nu < luminosity_nu_end)
@@ -439,7 +450,18 @@ def calculate_emitted_luminosity(
     def calculate_reabsorbed_luminosity(
         self, luminosity_nu_start, luminosity_nu_end
     ):
+        """
+        Calculate reabsorbed luminosity.
 
+        Parameters
+        ----------
+        luminosity_nu_start : astropy.units.Quantity
+        luminosity_nu_end : astropy.units.Quantity
+
+        Returns
+        -------
+        astropy.units.Quantity
+        """
         luminosity_wavelength_filter = (
             self.reabsorbed_packet_nu > luminosity_nu_start
         ) & (self.reabsorbed_packet_nu < luminosity_nu_end)
@@ -484,6 +506,17 @@ def calculate_radiationfield_properties(self):
         return t_rad * u.K, w
 
     def calculate_luminosity_inner(self, model):
+        """
+        Calculate inner luminosity.
+
+        Parameters
+        ----------
+        model : model.Radial1DModel
+
+        Returns
+        -------
+        astropy.units.Quantity
+        """
         return (
             4
             * np.pi
@@ -493,6 +526,17 @@ def calculate_luminosity_inner(self, model):
         ).to("erg/s")
 
     def calculate_time_of_simulation(self, model):
+        """
+        Calculate time of montecarlo simulation.
+
+        Parameters
+        ----------
+        model : model.Radial1DModel
+
+        Returns
+        -------
+        float
+        """
         return 1.0 * u.erg / self.calculate_luminosity_inner(model)
 
     def calculate_f_nu(self, frequency):
@@ -502,13 +546,14 @@ def calculate_f_lambda(self, wavelength):
         pass
 
     @classmethod
-    def from_config(cls, config, packet_source=None):
+    def from_config(cls, config, packet_source=None, virtual_packet_logging=False):
         """
         Create a new MontecarloRunner instance from a Configuration object.
 
         Parameters
         ----------
         config : tardis.io.config_reader.Configuration
+        virtual_packet_logging : bool
 
         Returns
         -------
@@ -552,5 +597,5 @@ def from_config(cls, config, packet_source=None):
             debug_packets=config.montecarlo.debug_packets,
             logger_buffer=config.montecarlo.logger_buffer,
             single_packet_seed=config.montecarlo.single_packet_seed,
-            virtual_packet_logging=config.spectrum.virtual.virtual_packet_logging,
+            virtual_packet_logging=(config.spectrum.virtual.virtual_packet_logging | virtual_packet_logging),
         )

tardis/simulation/base.py

@@ -349,6 +349,9 @@ def iterate(self, no_of_packets, no_of_virtual_packets=0, last_run=False):
         self.iterations_executed += 1
 
     def run(self):
+        """
+        run the simulation
+        """
         start_time = time.time()
         while self.iterations_executed < self.iterations - 1:
             self.store_plasma_state(
@@ -502,13 +505,16 @@ def remove_callback(self, id):
             return False
 
     @classmethod
-    def from_config(cls, config, packet_source=None, **kwargs):
+    def from_config(
+        cls, config, packet_source=None, virtual_packet_logging=False, **kwargs
+    ):
         """
         Create a new Simulation instance from a Configuration object.
 
         Parameters
         ----------
         config : tardis.io.config_reader.Configuration
+
         **kwargs
             Allow overriding some structures, such as model, plasma, atomic data
             and the runner, instead of creating them from the configuration
@@ -541,7 +547,9 @@ def from_config(cls, config, packet_source=None, **kwargs):
             runner = kwargs["runner"]
         else:
             runner = MontecarloRunner.from_config(
-                config, packet_source=packet_source
+                config,
+                packet_source=packet_source,
+                virtual_packet_logging=virtual_packet_logging,
             )
 
         luminosity_nu_start = config.supernova.luminosity_wavelength_end.to(