Improve error flow catching in code

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

@@ -45,10 +45,10 @@ class Electrodynamics {
      \param ions Going to set the potential and aurora
    **/
 
-  int update(Planets planet,
-	     Grid gGrid,
-	     Times time,
-	     Ions &ions);
+  bool update(Planets planet,
+	      Grid gGrid,
+	      Times time,
+	      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

@@ -118,6 +118,7 @@ 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

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/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);
 

src/advance.cpp

@@ -10,18 +10,18 @@
 // so many inputs because it alters all of the states in the model.
 // -----------------------------------------------------------------------------
 
-int advance(Planets &planet,
-            Grid &gGrid,
-            Times &time,
-            Euv &euv,
-            Neutrals &neutrals,
-            Ions &ions,
-            Chemistry &chemistry,
-            Electrodynamics &electrodynamics,
-            Indices &indices,
-            Logfile &logfile) {
-
-  int iErr = 0;
+bool advance(Planets &planet,
+             Grid &gGrid,
+             Times &time,
+             Euv &euv,
+             Neutrals &neutrals,
+             Ions &ions,
+             Chemistry &chemistry,
+             Electrodynamics &electrodynamics,
+             Indices &indices,
+             Logfile &logfile) {
+
+  bool didWork = true;
 
   std::string function = "advance";
   static int iFunction = -1;
@@ -38,14 +38,13 @@ int advance(Planets &planet,
   gGrid.calc_sza(planet, time);
   neutrals.calc_mass_density();
   neutrals.calc_mean_major_mass();
-
   neutrals.calc_specific_heat();
   neutrals.calc_concentration();
   neutrals.calc_pressure();
   neutrals.calc_bulk_velocity();
   neutrals.calc_kappa_eddy();
-
   neutrals.calc_cMax();
+
   precision_t dtNeutral = neutrals.calc_dt(gGrid);
   precision_t dtIon = 100.0;
   time.calc_dt(dtNeutral, dtIon);
@@ -57,68 +56,81 @@ int advance(Planets &planet,
   // first
 
   neutrals.calc_scale_height(gGrid);
-  neutrals.set_bcs(gGrid, time, indices);
+  didWork = neutrals.set_bcs(gGrid, time, indices);
 
   if (input.get_nAltsGeo() > 1)
     neutrals.advect_vertical(gGrid, time);
 
   // ------------------------------------
   // Calculate source terms next:
 
-  iErr = calc_euv(planet,
-                  gGrid,
-                  time,
-                  euv,
-                  neutrals,
-                  ions,
-                  indices);
+  if (didWork)
+    didWork = calc_euv(planet,
+                       gGrid,
+                       time,
+                       euv,
+                       neutrals,
+                       ions,
+                       indices);
 
-  iErr = electrodynamics.update(planet,
-                                gGrid,
-                                time,
-                                ions);
-  calc_ion_neutral_coll_freq(neutrals, ions);
-  ions.calc_ion_drift(neutrals, gGrid, time.get_dt());
+  if (didWork)
+    didWork = electrodynamics.update(planet,
+                                     gGrid,
+                                     time,
+                                     ions);
 
-  calc_aurora(gGrid, neutrals, ions);
+  if (didWork) {
+    calc_ion_neutral_coll_freq(neutrals, ions);
+    ions.calc_ion_drift(neutrals, gGrid, time.get_dt());
 
-  // Calculate some neutral source terms:
-  neutrals.calc_conduction(gGrid, time);
-  chemistry.calc_chemistry(neutrals, ions, time, gGrid);
+    calc_aurora(gGrid, neutrals, ions);
 
-  if (input.get_O_cooling())
-    neutrals.calc_O_cool();
+    // Calculate some neutral source terms:
+    neutrals.calc_conduction(gGrid, time);
+    chemistry.calc_chemistry(neutrals, ions, time, gGrid);
 
-  if (input.get_NO_cooling())
-    neutrals.calc_NO_cool();
+    if (input.get_O_cooling())
+      neutrals.calc_O_cool();
 
-  neutrals.calc_conduction(gGrid, time);
-  chemistry.calc_chemistry(neutrals, ions, time, gGrid);
+    if (input.get_NO_cooling())
+      neutrals.calc_NO_cool();
 
-  neutrals.vertical_momentum_eddy(gGrid);
-  calc_ion_collisions(neutrals, ions);
-  calc_neutral_friction(neutrals);
+    neutrals.calc_conduction(gGrid, time);
+    chemistry.calc_chemistry(neutrals, ions, time, gGrid);
 
-  neutrals.add_sources(time);
+    neutrals.vertical_momentum_eddy(gGrid);
+    calc_ion_collisions(neutrals, ions);
+    calc_neutral_friction(neutrals);
 
-  ions.calc_ion_temperature(neutrals, gGrid, time);
-  ions.calc_electron_temperature(neutrals, gGrid);
+    neutrals.add_sources(time);
 
-  neutrals.exchange(gGrid);
+    ions.calc_ion_temperature(neutrals, gGrid, time);
+    ions.calc_electron_temperature(neutrals, gGrid);
 
-  time.increment_time();
+    if (input.get_is_cubesphere())
+      neutrals.exchange(gGrid);
+    else
+      neutrals.exchange_old(gGrid);
 
-  if (time.check_time_gate(input.get_dt_write_restarts())) {
-    report.print(3, "Writing restart files");
-    neutrals.restart_file(input.get_restartout_dir(), DoWrite);
-    ions.restart_file(input.get_restartout_dir(), DoWrite);
-    time.restart_file(input.get_restartout_dir(), DoWrite);
+    time.increment_time();
+
+    if (time.check_time_gate(input.get_dt_write_restarts())) {
+      report.print(3, "Writing restart files");
+      neutrals.restart_file(input.get_restartout_dir(), DoWrite);
+      ions.restart_file(input.get_restartout_dir(), DoWrite);
+      time.restart_file(input.get_restartout_dir(), DoWrite);
+    }
   }
 
-  iErr = output(neutrals, ions, gGrid, time, planet);
+  if (didWork)
+    didWork = output(neutrals, ions, gGrid, time, planet);
+
+  if (didWork)
+    didWork = logfile.write_logfile(indices, neutrals, ions, gGrid, time);
 
-  logfile.write_logfile(indices, neutrals, ions, gGrid, time);
+  if (!didWork)
+    report.error("Error in Advance!");
 
   report.exit(function);
-  return iErr;
+  return didWork;
 }