Merge pull request #17 from maryampatel/docs/fixdocs

Docs/fixdocs
tardis-sn · Nov 15, 2012 · dc85a81 · dc85a81
2 parents 1ac064c + d8db38e
commit dc85a81
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Showing 4 changed files with 51 additions and 11 deletions.
diff --git a/docs/tardis/atomic.rst b/docs/tardis/atomic.rst
@@ -6,9 +6,11 @@ All atomic data files are stored in an hdf5 file
 
 hdf5
 ----
-All atomic data are stored in hdf5 files, in tables. The atomic data table contains information on atomic number,
-symbol, mass; and the ionization data table contains atomic number, ion number, and ionization energy information.
-Tables contain attributes which contains units.
+All atomic data are stored in hdf5 files.
+The atomic data table contains information on atomic number, symbol, and masses.
+The ionization data table contains atomic number, ion number, and ionization energy information.
+The levels data table contains
+
 
 
 
@@ -40,6 +42,44 @@ Ionization Data
 | ionization energy      | Ionization Energy of atom    | eV       |
 +------------------------+------------------------------+----------+
 
+Levels Data
+
+
++------------------------+------------------------------+----------+
+|Name                    | Description                  | Symbol   |
++========================+==============================+==========+
+| atomic_number(z)       | Atomic Number                | 1        |
++------------------------+------------------------------+----------+
+| ion number             | Ion Number                   | 1        |
++------------------------+------------------------------+----------+
+| level number           | Level Number                 | 1        |
++------------------------+------------------------------+----------+
+| energy                 |                              |          |
++------------------------+------------------------------+----------+
+| g                      |                              |          |
++------------------------+------------------------------+----------+
+| metastable             |                              |          |
++------------------------+------------------------------+----------+
+
+Lines Data
+
++------------------------+------------------------------+----------+
+|Name                    | Description                  | Symbol   |
++========================+==============================+==========+
+| wavelength             |                              |          |
++------------------------+------------------------------+----------+
+| atomic_number(z)       | Atomic Number                | 1        |
++------------------------+------------------------------+----------+
+| ion number             | Ion Number                   | 1        |
++------------------------+------------------------------+----------+
+| f_ul                   |                              |          |
++------------------------+------------------------------+----------+
+| f_lu                   |                              |          |
++------------------------+------------------------------+----------+
+| level_id_l             |                              |          |
++------------------------+------------------------------+----------+
+| level_od_l             |                              |          |
++------------------------+------------------------------+----------+
 
 
 

diff --git a/docs/tardis/plasma.rst b/docs/tardis/plasma.rst
@@ -1,6 +1,5 @@
 Plasma
 ======
-
 .. currentmodule:: tardis.plasma
 
 Level Populations
@@ -10,7 +9,6 @@ We first calculate the number densities for each atom
 :math:`N_{atom} = \rho_\textrm{total} \times \textrm{Abundance fraction} / m_\textrm{atom}`
 
 Next we calculate the partition function (Z) where i is the level number and j the ion number:
-
 :math:`Z_{j} = \sum_{i=0}^{max levels} g_i * e^{-E_i / (k_\textrm{b} T)}`
 
 .. automodapi:: tardis.plasma
diff --git a/tardis/atomic.py b/tardis/atomic.py
@@ -119,7 +119,8 @@ def read_ionization_data(fname=None):
 
 
 def read_levels_data(fname=None):
-    """This function reads the atomic number, ion number, and ionization energy from hdf5 file
+    """This function reads atomic number, ion number, level_number, energy, g, metastable
+    information from hdf5 file.
 
     Parameters
     ----------
@@ -131,8 +132,7 @@ def read_levels_data(fname=None):
     -------
 
     data : `~astropy.table.Table`
-        table with fields ### FILL IN DATA###
-
+        table with fields z[1], ion[1], level_number, energy, g, metastable
     """
 
     data_table = read_hdf5_data(fname, 'levels_data')
@@ -143,7 +143,8 @@ def read_levels_data(fname=None):
 
 
 def read_lines_data(fname=None):
-    """This function reads the atomic number, ion number, and ionization energy from hdf5 file
+    """This function reads the wavelength, atomic number, ion number, f_ul, f_l and level id information
+     from hdf5 file
 
     Parameters
     ----------

diff --git a/tardis/plasma.py b/tardis/plasma.py
@@ -68,8 +68,9 @@ def _calculate_atom_number_densities(self):
     def calculate_partition_functions(self, temperature):
         """
         Calculate partition functions for the ions using the following formula:
-        .. math::
-            Z_{j} = \sum_{i=0}^{max(levels)} g_i * e^{-E_i / (k_\textrm{b} T)}
+
+        :math:`Z_{j} = \\sum_{i=0}^{max levels} g_i \\times e^{-E_i / (k_\\textrm{b} T)}`
+
 
         Parameters
         ----------