Merge pull request #182 from AetherModel/data_assimilation

Cleaning up the restarts - this is good stuff for making the grids work together.  Before moving to the next project, I want to get all of this stuff into the develop branch.

Author: aaronjridley

include/advance.h

@@ -33,20 +33,20 @@
 
 
 bool advance(Planets &planet,
-	     Grid &gGrid,
-	     Grid &mGrid,
-	     Times &time,
-	     Euv &euv,
-	     Neutrals &neutrals,
-	     Neutrals &neutralsMag,
-	     Ions &ions,
-	     Ions &ionsMag,
-	     Chemistry &chemistry,
-	     Chemistry &chemistryMag,
-	     Electrodynamics &electrodynamics,
-	     Electrodynamics &electrodynamicsMag,
-	     Indices &indices,
-	     Logfile &logfile,
-	     Logfile &logfileMag);
+             Grid &gGrid,
+             Grid &mGrid,
+             Times &time,
+             Euv &euv,
+             Neutrals &neutrals,
+             Neutrals &neutralsMag,
+             Ions &ions,
+             Ions &ionsMag,
+             Chemistry &chemistry,
+             Chemistry &chemistryMag,
+             Electrodynamics &electrodynamics,
+             Electrodynamics &electrodynamicsMag,
+             Indices &indices,
+             Logfile &logfile,
+             Logfile &logfileMag);
 
 #endif // INCLUDE_ADVANCE_H_

include/aurora.h

@@ -12,16 +12,16 @@
  **/
 
 void read_aurora(Neutrals &neutrals,
-		 Ions &ions);
+                 Ions &ions);
 
 arma_vec calculate_fang(float eflux,  // in ergs/cm2/s
-			float avee,   // in keV
-			float Ebin,   // eV
-			arma_vec rhoH,
-			std::vector<float> Ci,
-			float dE,     // eV
-			arma_vec H,
-			bool DoDebug);
+                        float avee,   // in keV
+                        float Ebin,   // eV
+                        arma_vec rhoH,
+                        std::vector<float> Ci,
+                        float dE,     // eV
+                        arma_vec H,
+                        bool DoDebug);
 
 /**********************************************************************
   * brief Read in a file containing information about splitting ionization
@@ -32,7 +32,7 @@ arma_vec calculate_fang(float eflux,  // in ergs/cm2/s
  **/
 
 void calc_aurora(Grid grid,
-		 Neutrals &neutrals,
-		 Ions &ions);
+                 Neutrals &neutrals,
+                 Ions &ions);
 
 #endif  // INCLUDE_AURORA_H_

include/bfield.h

@@ -11,18 +11,18 @@ struct bfield_info_type {
 };
 
 arma_vec get_magnetic_pole(int IsNorth,
-		       Planets planet);
+                           Planets planet);
 
 bfield_info_type get_bfield(precision_t lon,
                             precision_t lat,
                             precision_t alt,
-			    bool DoDebug,
+                            bool DoDebug,
                             Planets planet);
 
 bfield_info_type get_dipole(precision_t lon,
                             precision_t lat,
                             precision_t alt,
-			    bool DoDebug,
+                            bool DoDebug,
                             Planets planet);
 
 #endif // INCLUDE_BFIELD_H_

include/calc_euv.h

@@ -21,16 +21,16 @@
 // -------------------------------------------------------------------------
 
 bool calc_euv(Planets planet,
-	      Grid grid,
-	      Times time,
-	      Euv &euv,
-	      Neutrals &neutrals,
-	      Ions &ions,
-	      Indices indices);
+              Grid grid,
+              Times time,
+              Euv &euv,
+              Neutrals &neutrals,
+              Ions &ions,
+              Indices indices);
 
 void calc_ionization_heating(Euv euv,
-			     Neutrals &neutrals,
-			     Ions &ions);
+                             Neutrals &neutrals,
+                             Ions &ions);
 
 
 #endif  // INCLUDE_CALC_EUV_H_

include/calc_grid_derived.h

@@ -7,7 +7,7 @@
 #include <vector>
 
 // ----------------------------------------------------------------------------
-// 
+//
 // ----------------------------------------------------------------------------
 
 std::vector<precision_t> calc_bin_edges(std::vector<precision_t> centers);
@@ -19,8 +19,8 @@ arma_vec calc_bin_widths(arma_vec centers);
 // ----------------------------------------------------------------------------
 // A helper function for mapping grids
 // ----------------------------------------------------------------------------
-bool grid_match(Grid gGrid, 
-                Grid mGrid, 
+bool grid_match(Grid gGrid,
+                Grid mGrid,
                 Quadtree gQuadtree,
                 Quadtree mQuadtree);
 

include/chemistry.h

@@ -72,7 +72,7 @@ class Chemistry {
     /// type of formula to use for reaction rate:
     int type;
     /// name of the reaction
-    std::string name;    
+    std::string name;
 
   };
 
@@ -93,12 +93,12 @@ class Chemistry {
                              Ions &ions);
 
  private:
-  bool search(std::string name, 
-              json &headers, 
+  bool search(std::string name,
+              json &headers,
               std::vector<std::string> &error);
 
-  bool check_chemistry_file(json &headers, 
-                            std::vector<std::vector<std::string>> csv, 
+  bool check_chemistry_file(json &headers,
+                            std::vector<std::vector<std::string>> csv,
                             Report &report);
 
   int read_chemistry_file(Neutrals neutrals,
@@ -107,7 +107,7 @@ class Chemistry {
   reaction_type interpret_reaction_line(const Neutrals &neutrals,
                                         const Ions &ions,
                                         const std::vector<std::string> &line,
-					const json &headers);
+                                        const json &headers);
 
   void find_species_id(const std::string &name,
                        const Neutrals &neutrals,

include/collisions.h

@@ -11,6 +11,6 @@
 #include "ions.h"
 
 void calc_ion_neutral_coll_freq(Neutrals &neutrals,
-                 Ions &ions);
+                                Ions &ions);
 
 #endif  // INCLUDE_COLLISIONS_H_

include/constants.h

@@ -6,6 +6,18 @@
 
 #include <vector>
 
+// -------------------------------------------------------------------------
+// Define some constants for the code so that all functions understand
+// stuff
+// These are not physical constants, but are useful references
+// -------------------------------------------------------------------------
+
+const int iSphere_ = 1;
+const int iCubesphere_ = 2;
+const int iDipole_ = 3;
+const std::string neutralType_ = "neuGrid";
+const std::string ionType_ = "ionGrid";
+
 // -------------------------------------------------------------------------
 // Physical Constants
 //   - Naming standards:
@@ -65,7 +77,7 @@ const double cJULIAN2000 = 2451545.0;
 // -------------------------------------------------------------------------
 
 const precision_t cPI = 3.141592653589793;
-const precision_t cTWOPI = 2*cPI;
+const precision_t cTWOPI = 2 * cPI;
 
 // -------------------------------------------------------------------------
 // Conversion Constants:
@@ -75,8 +87,8 @@ const precision_t cTWOPI = 2*cPI;
 //   - Names are all UPPER CASE otherwise
 // -------------------------------------------------------------------------
 
-const precision_t cDtoR = cPI/180.0;
-const precision_t cRtoD = 180.0/cPI;
+const precision_t cDtoR = cPI / 180.0;
+const precision_t cRtoD = 180.0 / cPI;
 
 // -------------------------------------------------------------------------
 // converting time between seconds and other units of time:
@@ -99,7 +111,7 @@ const double cMtoS = 60.0;
 const double cStoM = 1.0 / cMtoS;
 
 // MilliSeconds <-> Seconds:
-const double cMStoS = 1.0/1000.0;
+const double cMStoS = 1.0 / 1000.0;
 const double cStoMS = 1000.0;
 
 // -------------------------------------------------------------------------