STY: Finish moving e- temp into Ions class

Author: abukowski21

include/ions.h

@@ -357,31 +357,28 @@ class Ions {
   /// @details intermediate variable used in photoelectron & ionization heating
   /// From (Smithro & Solomon, 2008).
   /// @param neutrals 
-  /// @param ions 
   /// @return epsilon
   **/
-  arma_cube calc_epsilon(Neutrals &neutrals, Ions &ions);
+  arma_cube calc_epsilon(Neutrals &neutrals);
 
   /**********************************************************************
     \brief Calculates photoelectron heating
     \details Based on (Swartz & Nisbet, 1972) & (Smithro & Solomon, 2008)
             Uses equations 9-12 from (Zhu & Ridley, 2016)
             https://doi.org/10.1016/j.jastp.2016.01.005
-    \param ions 
     \param epsilon 
     \return Qphe 
   **/
-  arma_cube calc_photoelectron_heating(Ions &ions, arma_cube epsilon);
+  arma_cube calc_photoelectron_heating(arma_cube epsilon);
 
   /**********************************************************************
     \brief Calculates auroral heating
     \details NOTE: in GITM this is solved separately for ion precipitation & auroral 
         ionization. In Aether these are both in ions.species[iIon].ionization_scgc...
-    \param ions 
     \param epsilon 
     \return Qaurora 
   **/
-  arma_cube calc_ionization_heating(Ions &ions, arma_cube epsilon);
+  arma_cube calc_ionization_heating(arma_cube epsilon);
 
   /**********************************************************************
     \brief Calculates electron-ion (elastic) collisional heating
@@ -390,31 +387,27 @@ class Ions {
       Instead, here we use each ion species for the sum.
     - electon-ion collision frequency (from Schunk and Nagy 2009) = 5.45E-5
     - This is capable of handling BOTH the bulk & individual ion temperatures
-    \param ions 
     \return vector<Qeicp, Qeicm, Qeic_v>
   **/
-  std::vector<arma_cube> calc_electron_ion_collisions(Ions &ions);
+  std::vector<arma_cube> calc_electron_ion_collisions();
 
   /**********************************************************************
     \brief Calculates electron-neutral elastic collisional heating
     \details From Schunk and Nagy 2009
-    \param ions 
     \param neutrals 
     \return vector<Qencp, Qencm, Qenc_v>
   **/
-  std::vector<arma_cube> calc_electron_neutral_elastic_collisions(Ions &ions, Neutrals &neutrals);
+  std::vector<arma_cube> calc_electron_neutral_elastic_collisions(Neutrals &neutrals);
 
   /**********************************************************************
     \brief Calculates the electron-neutral inelastic collisional heating
     \details From Schunk and Nagy 2009 pages 277, 282.
     This includes N2, O2 rotation, fine structure, O(1D) exitation & vibration, N2 vibration.
     See equation 15 from (Zhu, Ridley, Deng, 2016) https://doi.org/10.1016/j.jastp.2016.01.005
-    \param ions 
     \param neutrals 
     \return vector<Qencp, Qencm, Qenc_v>
   **/
-  std::vector<arma_cube> calc_electron_neutral_inelastic_collisions(Ions &ions, Neutrals &neutrals);
-
+  std::vector<arma_cube> calc_electron_neutral_inelastic_collisions(Neutrals &neutrals);
 
   /**********************************************************************
      \brief Check all of the variables for nonfinites, such as nans

src/advance.cpp

@@ -200,9 +200,9 @@ bool advance(Planets &planet,
     }
 
     ions.calc_ion_temperature(neutrals, gGrid, time);
-    ions.calc_electron_temperature(neutrals, gGrid, time);
+    // ions.calc_electron_temperature(neutrals, gGrid, time);
     //ionsMag.calc_ion_temperature(neutralsMag, mGrid, time);
-    //ionsMag.calc_electron_temperature(neutralsMag, mGrid);
+    ionsMag.calc_electron_temperature(neutralsMag, mGrid, time);
 
     if (didWork & input.get_check_for_nans())
       didWork = neutrals.check_for_nonfinites("After Vertical Advection");