Merge pull request #143 from AetherModel/develop

Update so I can debug

CMakeLists.txt

@@ -31,6 +31,8 @@ elseif(TEST_COORD)
 elseif(TEST_EXCHANGE)
   add_executable(aether ${SRC_FILES} ${MSIS_FILES} ${IE_FILES} ${MAIN_DIR}/main_test_exchange.cpp)
   set(USE_DOUBLE_PRECISION True)
+elseif(TEST_GRADIENT)
+  add_executable(aether ${SRC_FILES} ${MSIS_FILES} ${MAIN_DIR}/main_test_gradient.cpp)
 else()
   add_executable(aether ${SRC_FILES} ${MSIS_FILES} ${IE_FILES} ${MAIN_DIR}/main.cpp)
 endif()

include/advance.h

@@ -32,15 +32,15 @@
  **/
 
 
-int advance(Planets &planet,
-            Grid &gGrid,
-            Times &time,
-            Euv &euv,
-            Neutrals &neutrals,
-            Ions &ions,
-            Chemistry &chemistry,
-            Electrodynamics &electrodynamics,
-            Indices &indices,
-            Logfile &logfile);
+bool advance(Planets &planet,
+	     Grid &gGrid,
+	     Times &time,
+	     Euv &euv,
+	     Neutrals &neutrals,
+	     Ions &ions,
+	     Chemistry &chemistry,
+	     Electrodynamics &electrodynamics,
+	     Indices &indices,
+	     Logfile &logfile);
 
 #endif // INCLUDE_ADVANCE_H_

include/calc_euv.h

@@ -20,13 +20,13 @@
 //
 // -------------------------------------------------------------------------
 
-int calc_euv(Planets planet,
-             Grid grid,
-             Times time,
-             Euv &euv,
-             Neutrals &neutrals,
-             Ions &ions,
-             Indices indices);
+bool calc_euv(Planets planet,
+	      Grid grid,
+	      Times time,
+	      Euv &euv,
+	      Neutrals &neutrals,
+	      Ions &ions,
+	      Indices indices);
 
 void calc_ionization_heating(Euv euv,
 			     Neutrals &neutrals,

include/electrodynamics.h

@@ -67,11 +67,12 @@ class Electrodynamics {
      \param ions Going to set the potential and aurora
    **/
 
-  int update(Planets planet,
-	     Grid gGrid,
-	     Times time,
-       Indices &indices,
-	     Ions &ions);
+  bool update(Planets planet,
+	      Grid gGrid,
+	      Times time,
+        Indices &indices,
+        Ions &ions);
+
 
   /**************************************************************
      \brief used in main.cpp to ensure electrodynamics times and

include/euv.h

@@ -107,28 +107,28 @@ class Euv {
      \param time The times within the model (dt is needed)
      \param indices Need the F107 and F107a
    **/
-  int euvac(Times time, Indices indices);
+  bool euvac(Times time, Indices indices);
 
  /**********************************************************************
      \brief Compute the EUV spectrum given F107 and F107a
      \param time The times within the model (dt is needed)
      \param indices Need the F107 and F107a
    **/
-  int solomon_hfg(Times time, Indices indices);
+ bool solomon_hfg(Times time, Indices indices);
 
   /**********************************************************************
      \brief Compute the EUV spectrum given F107 and F107a (new version)
      \param time The times within the model (dt is needed)
      \param indices Need the F107 and F107a
    **/
-  int neuvac(Times time, Indices indices);
+  bool neuvac(Times time, Indices indices);
 
   /**********************************************************************
      \brief Scale the EUV spectrum given the star - planet distance
      \param planet needed to compute the star - planet distance
      \param time Needed to compute orbital position around star
    **/
-  int scale_from_1au(Planets planet, Times time);
+  void scale_from_1au(Planets planet, Times time);
 
   /**********************************************************************
      \brief Pairs rows in the EUV CSV file with neutral and ions
@@ -142,8 +142,7 @@ class Euv {
      \param neutrals Needs names of the neutrals, stores lines in Neutrals
      \param ions Needs names of the ions
    **/
-  bool pair_euv(Neutrals &neutrals,
-		Ions ions);
+  bool pair_euv(Neutrals &neutrals, Ions ions);
 
   /**********************************************************************
      \brief Check to see if internal state of class is ok

include/inputs.h

@@ -123,6 +123,7 @@ class Inputs {
 
   std::string get_settings_str(std::string key1);
   std::string get_settings_str(std::string key1, std::string key2);
+  int get_settings(std::string key1, std::string key2);
   bool check_settings(std::string key1, std::string key2);
   bool check_settings(std::string key1);
   std::string check_settings_str(std::string key1, std::string key2);

include/neutrals.h

@@ -257,9 +257,9 @@ class Neutrals {
      \param time contains information about the current time
      \param indices used to help set initial conditions
    **/
-  int initial_conditions(Grid grid,
-			 Times time,
-			 Indices indices);
+  bool initial_conditions(Grid grid,
+			  Times time,
+			  Indices indices);
 
   /**********************************************************************
      \brief temporary function to set neutral densities with in the model
@@ -339,15 +339,8 @@ class Neutrals {
      \param grid The grid to define the neutrals on
    **/
   precision_t calc_dt(Grid grid);
-
-  /**********************************************************************
-     \brief Calculate dt (cell size / cMax) in each direction, and take min
-     \param dt returns the neutral time-step
-     \param grid The grid to define the neutrals on
-     This function is for cubesphere dt calculation only
-   **/
   precision_t calc_dt_cubesphere(Grid grid);
-  
+
   /**********************************************************************
      \brief Calculate the chapman integrals for the individual species
      \param grid The grid to define the neutrals on

include/output.h

@@ -122,22 +122,22 @@ class OutputContainer {
   /**********************************************************************
      \brief write a file with the information in the container
    **/
-  void write();
+  bool write();
 
   /**********************************************************************
      \brief write a json header file with the information in the container
    **/
-  int write_container_header();
+  bool write_container_header();
 
   /**********************************************************************
      \brief write a binary file with the information in the container
    **/
-  int write_container_binary();
+  bool write_container_binary();
 
   /**********************************************************************
      \brief write a netcdf file with the information in the container
    **/
-  int write_container_netcdf();
+  bool write_container_netcdf();
 
   /**********************************************************************
      \brief read from a file an load into the container
@@ -222,11 +222,11 @@ class OutputContainer {
    \param planet information about the planet
 **/
 
-int output(const Neutrals &neutrals,
-	   const Ions &ions,
-	   const Grid &grid,
-	   Times time,
-	   const Planets &planet);
+bool output(const Neutrals &neutrals,
+	    const Ions &ions,
+	    const Grid &grid,
+	    Times time,
+	    const Planets &planet);
 
 void output_binary_3d(std::ofstream &binary,
 		      arma_cube value);

include/solvers.h

@@ -56,6 +56,7 @@ arma_cube calc_gradient_lon(arma_cube value, Grid grid);
 arma_cube calc_gradient_lat(arma_cube value, Grid grid);
 arma_cube calc_gradient_alt(arma_cube value, Grid grid);
 std::vector<arma_cube> calc_gradient_vector(arma_cube value_scgc, Grid grid);
+std::vector<arma_cube> calc_gradient_cubesphere(arma_cube value, Grid grid);
 arma_cube calc_gradient_alt_4th(arma_cube value, Grid grid);
 
 // interpolation in 1D

include/tools.h

@@ -15,6 +15,13 @@ struct mat_2x2{
     arma_mat A22;
 };
 
+// -----------------------------------------------------------------------------
+// add cMember into a string just before last period
+// -----------------------------------------------------------------------------
+
+std::string add_cmember(std::string inString);
+
+
 // ----------------------------------------------------------------------
 // Display an armadillo vector
 // ----------------------------------------------------------------------

include/transform.h

@@ -10,6 +10,9 @@
 #include "aether.h"
 using namespace arma;
 
+std::string mklower(std::string inString);
+std::string mkupper(std::string inString);
+
 void copy_cube_to_array(arma_cube cube_in,
                         float *array_out);
 void copy_mat_to_array(arma_mat mat_in,