Reintroduce and adjust various to_hdf methods.

tardis/model/base.py

@@ -6,6 +6,7 @@
 
 from tardis.util import quantity_linspace, element_symbol2atomic_number
 from tardis.io.model_reader import read_density_file, read_abundances_file
+from tardis.io.util import to_hdf
 from density import HomologousDensity
 
 logger = logging.getLogger(__name__)
@@ -192,6 +193,27 @@ def v_boundary_outer_index(self):
             return None
         return self.raw_velocity.searchsorted(self.v_boundary_outer) + 1
 
+    def to_hdf(self, path_or_buf, path=''):
+        """
+        Store the model to an HDF structure.
+
+        Parameters
+        ----------
+        path_or_buf
+            Path or buffer to the HDF store
+        path : str
+            Path inside the HDF store to store the model
+
+        Returns
+        -------
+        None
+
+        """
+        model_path = os.path.join(path, 'model')
+        properties = ['t_inner', 'w', 't_radiative', 'v_inner', 'v_outer']
+        to_hdf(path_or_buf, model_path, {name: getattr(self, name) for name
+                                         in properties})
+
     @classmethod
     def from_config(cls, config):
         time_explosion = config.supernova.time_explosion.cgs

tardis/plasma/base.py

@@ -290,3 +290,7 @@ def to_hdf(self, path_or_buf, path='', collection=None):
             properties = self.plasma_properties
         for prop in properties:
             prop.to_hdf(path_or_buf, os.path.join(path, 'plasma'))
+
+        metadata = pd.Series({'atom_data_uuid': self.atomic_data.uuid1})
+        metadata.to_hdf(path_or_buf,
+                        os.path.join(os.path.join(path, 'plasma'), 'metadata'))

tardis/simulation/base.py

@@ -235,6 +235,28 @@ def log_run_results(self, emitted_luminosity, absorbed_luminosity):
             emitted_luminosity, absorbed_luminosity,
             self.luminosity_requested))
 
+    def to_hdf(self, path_or_buf, path='', plasma_properties=None):
+        """
+        Store the simulation to an HDF structure.
+
+        Parameters
+        ----------
+        path_or_buf
+            Path or buffer to the HDF store
+        path : str
+            Path inside the HDF store to store the simulation
+        plasma_properties
+            `None` or a `PlasmaPropertyCollection` which will
+            be passed as the collection argument to the
+            plasma.to_hdf method.
+        Returns
+        -------
+        None
+        """
+        self.runner.to_hdf(path_or_buf, path)
+        self.model.to_hdf(path_or_buf, path)
+        self.plasma.to_hdf(path_or_buf, path, plasma_properties)
+
     @classmethod
     def from_config(cls, config):
         model = Radial1DModel.from_config(config)