Armadillo

edu/examples/arm.cpp

@@ -10,7 +10,7 @@
  is each to use these 3d arrys.
 
  Here is how I compiled the code (clearly, I installed it in /usr/local):
- g++ arm.cpp -o arm.exe -std=c++11 -O2 -larmadillo -I/usr/local/include -L/usr/local/lib
+ g++ arm.cpp -o arm.exe -std=c++11 -O2 -larmadillo -I/usr/local/include
 
 */
 

include/advance.h

@@ -1,8 +1,8 @@
-// (c) 2020, the Aether Development Team (see doc/dev_team.md for members)
+// Copyright 2020, the Aether Development Team (see doc/dev_team.md for members)
 // Full license can be found in License.md
 
-#ifndef AETHER_INCLUDE_ADVANCE_H_
-#define AETHER_INCLUDE_ADVANCE_H_
+#ifndef INCLUDE_ADVANCE_H_
+#define INCLUDE_ADVANCE_H_
 
 #include "../include/times.h"
 #include "../include/inputs.h"
@@ -12,15 +12,15 @@
 #include "../include/planets.h"
 #include "../include/ions.h"
 
-int advance( Planets &planet,
-	     Grid &gGrid,
-	     Times &time,
-	     Euv &euv,
-	     Neutrals &neutrals,
-	     Ions &ions,
-	     Chemistry &chemistry,
-	     Indices &indices,
-	     Inputs &args,
-	     Report &report);
+int advance(Planets &planet,
+            Grid &gGrid,
+            Times &time,
+            Euv &euv,
+            Neutrals &neutrals,
+            Ions &ions,
+            Chemistry &chemistry,
+            Indices &indices,
+            Inputs &args,
+            Report &report);
 
-#endif // AETHER_INCLUDE_ADVANCE_H_
+#endif // INCLUDE_ADVANCE_H_

include/bfield.h

@@ -1,8 +1,12 @@
-// (c) 2020, the Aether Development Team (see doc/dev_team.md for members)
+// Copyright 2020, the Aether Development Team (see doc/dev_team.md for members)
 // Full license can be found in License.md
 
-#ifndef AETHER_INCLUDE_BFIELD_H_
-#define AETHER_INCLUDE_BFIELD_H_
+#ifndef INCLUDE_BFIELD_H_
+#define INCLUDE_BFIELD_H_
+
+#include "../include/planets.h"
+#include "../include/inputs.h"
+#include "../include/report.h"
 
 struct bfield_info_type {
   float b[3];
@@ -11,25 +15,24 @@ struct bfield_info_type {
 };
 
 bfield_info_type get_bfield(float lon,
-			    float lat,
-			    float alt,
-			    Planets planet,
-			    Inputs input,
-			    Report &report);
+                            float lat,
+                            float alt,
+                            Planets planet,
+                            Inputs input,
+                            Report &report);
 
 bfield_info_type get_dipole(float lon,
-			    float lat,
-			    float alt,
-			    Planets planet,
-			    Inputs input,
-			    Report &report);
+                            float lat,
+                            float alt,
+                            Planets planet,
+                            Inputs input,
+                            Report &report);
 
 bfield_info_type get_dipole(float lon,
-			    float lat,
-			    float alt,
-			    Planets planet,
-			    Inputs input,
-			    Report &report);
-
-#endif // AETHER_INCLUDE_EUV_H_
+                            float lat,
+                            float alt,
+                            Planets planet,
+                            Inputs input,
+                            Report &report);
 
+#endif // INCLUDE_EUV_H_

include/calc_chemistry.h

@@ -1,61 +1,49 @@
-// (c) 2020, the Aether Development Team (see doc/dev_team.md for members)
+// Copyright 2020, the Aether Development Team (see doc/dev_team.md for members)
 // Full license can be found in License.md
 
-#ifndef AETHER_INCLUDE_CALC_CHEMISTRY_H_
-#define AETHER_INCLUDE_CALC_CHEMISTRY_H_
+#ifndef INCLUDE_CALC_CHEMISTRY_H_
+#define INCLUDE_CALC_CHEMISTRY_H_
+
+#include <vector>
+#include <string>
+#include "../include/ions.h"
+#include "../include/neutrals.h"
+#include "../include/times.h"
+#include "../include/grid.h"
+#include "../include/report.h"
 
 class Chemistry {
 
  public:
 
   Chemistry(Inputs args, Report report);
-
-  struct reaction_type {
 
+  struct reaction_type {
     // Reactions:
     // loss1 + loss2 + loss3 -> source1 + source2 + source3
-  
+
     std::vector<std::string> sources_names;
     std::vector<std::string> losses_names;
-    
+
     std::vector<int> sources_ids;
     std::vector<int> sources_IsNeutrals;
-  
+
     std::vector<int> losses_ids;
     std::vector<int> losses_IsNeutrals;
 
     float rate;
-
   };
 
   std::vector<reaction_type> reactions;
-
-  struct sources_and_losses_type {
 
+  struct sources_and_losses_type {
     float neutral_sources[nSpecies];
     float neutral_losses[nSpecies];
     float ion_sources[nIons];
     float ion_losses[nIons];
-
     float heat_neutrals;
     float heat_ions;
     float heat_electrons;
-
   };
 
-  void calc_chemistry(Neutrals &neutrals,
-		      Ions &ions,
-		      Times time,
-		      Grid grid,
-		      Report report);
-
-  void calc_chemical_sources(float neutral_density,
-			     float ion_density,
-			     float Tn,
-			     float Ti,
-			     float Te,
-			     sources_and_losses_type &sources_and_losses;
-			     Report report);
-
-
-#endif // AETHER_INCLUDE_CALC_CHEMISTRY_H_
+#endif  // INCLUDE_CALC_CHEMISTRY_H_

include/calc_euv.h

@@ -1,8 +1,8 @@
-// (c) 2020, the Aether Development Team (see doc/dev_team.md for members)
+// Copyright 2020, the Aether Development Team (see doc/dev_team.md for members)
 // Full license can be found in License.md
 
-#ifndef AETHER_INCLUDE_CALC_EUV_H_
-#define AETHER_INCLUDE_CALC_EUV_H_
+#ifndef INCLUDE_CALC_EUV_H_
+#define INCLUDE_CALC_EUV_H_
 
 #include <vector>
 #include <string>
@@ -20,14 +20,14 @@
 //
 // -------------------------------------------------------------------------
 
-int calc_euv( Planets planet,
-	      Grid grid,
-	      Times time,
-	      Euv &euv,
-	      Neutrals &neutrals,
-	      Ions &ions,
-	      Indices indices,
-	      Inputs args,
-	      Report &report);
+int calc_euv(Planets planet,
+             Grid grid,
+             Times time,
+             Euv &euv,
+             Neutrals &neutrals,
+             Ions &ions,
+             Indices indices,
+             Inputs args,
+             Report &report);
 
-#endif // AETHER_INCLUDE_CALC_EUV_H_
+#endif  // INCLUDE_CALC_EUV_H_

include/chemistry.h

@@ -1,8 +1,8 @@
-// (c) 2020, the Aether Development Team (see doc/dev_team.md for members)
+// Copyright 2020, the Aether Development Team (see doc/dev_team.md for members)
 // Full license can be found in License.md
 
-#ifndef AETHER_INCLUDE_CHEMISTRY_H_
-#define AETHER_INCLUDE_CHEMISTRY_H_
+#ifndef INCLUDE_CHEMISTRY_H_
+#define INCLUDE_CHEMISTRY_H_
 
 #include <vector>
 #include <string>
@@ -13,55 +13,47 @@
 #include "../include/inputs.h"
 #include "../include/report.h"
 
-
 class Chemistry {
 
  public:
 
   struct reaction_type {
-
     // Reactions:
     // loss1 + loss2 + loss3 -> source1 + source2 + source3
-
     std::vector<std::string> sources_names;
     std::vector<std::string> losses_names;
-    
+
     std::vector<int> sources_ids;
     std::vector<int> sources_IsNeutral;
-  
+
     std::vector<int> losses_ids;
     std::vector<int> losses_IsNeutral;
 
     int nSources;
     int nLosses;
-    
+
     float energy;
     float rate;
     float branching_ratio;
-
   };
 
   std::vector<reaction_type> reactions;
-  long nReactions;
-  
+  int64_t nReactions;
+
   Chemistry(Neutrals neutrals,
-	    Ions ions,
-	    Inputs args,
-	    Report &report);
+            Ions ions,
+            Inputs args,
+            Report &report);
 
-
   void calc_chemistry(Neutrals &neutrals,
-		      Ions &ions,
-		      Times time,
-		      Grid grid,
-		      Report &report);
-
-  void calc_chemical_sources(float *neutral_density,
-			     float *ion_density,
-			     float Tn,
-			     float Ti,
-			     float Te,
-			     Report &report);
+                      Ions &ions,
+                      Times time,
+                      Grid grid,
+                      Report &report);
+
+  void calc_chemical_sources(Neutrals &neutrals,
+                             Ions &ions,
+                             Report &report);
 
  private:
 
@@ -71,36 +63,32 @@ class Chemistry {
     float neutral_losses[nSpecies];
     float ion_sources[nIons];
     float ion_losses[nIons];
-    
+
     float heat_neutrals;
     float heat_ions;
     float heat_electrons;
-
   };
 
   sources_and_losses_type sources_and_losses;
-  
+
   int read_chemistry_file(Neutrals neutrals,
-			  Ions ions,
-			  Inputs args,
-			  Report &report);
-  
+                          Ions ions,
+                          Inputs args,
+                          Report &report);
+
   reaction_type interpret_reaction_line(Neutrals neutrals,
-					Ions ions,
-					std::vector<std::string> line,
-					Report &report);
+                                        Ions ions,
+                                        std::vector<std::string> line,
+                                        Report &report);
 
   void find_species_id(std::string name,
-		       Neutrals neutrals,
-		       Ions ions,
-		       int &id_,
-		       int &IsNeutral,
-		       Report &report);
+                       Neutrals neutrals,
+                       Ions ions,
+                       int &id_,
+                       int &IsNeutral,
+                       Report &report);
 
   void display_reaction(reaction_type reaction);
-
-
-
 };
 
-#endif // AETHER_INCLUDE_CHEMISTRY_H_
+#endif  // INCLUDE_CHEMISTRY_H_