STY: Astyle, yo!

src/add_sources.cpp

@@ -24,24 +24,24 @@ void Neutrals::add_sources(Times time) {
                            + conduction_scgc
                            - O_cool_scgc
                            - NO_cool_scgc);
-  
+
   for (int64_t iSpec = 0; iSpec < nSpecies; iSpec++) {
     for (int iDir = 0; iDir < 3; iDir++) {
       // update velocities based on acceleration:
       // reduce neutral friction until solver is added
       species[iSpec].velocity_vcgc[iDir] =
         species[iSpec].velocity_vcgc[iDir] +
-        dt * (species[iSpec].acc_neutral_friction[iDir] / 4.0 + 
-	      species[iSpec].acc_ion_drag[iDir]);
+        dt * (species[iSpec].acc_neutral_friction[iDir] / 4.0 +
+              species[iSpec].acc_ion_drag[iDir]);
 
       // eddy acceleration is only in the vertical direction:
       if (iDir == 2)
         species[iSpec].velocity_vcgc[iDir] =
           species[iSpec].velocity_vcgc[iDir] +
-            dt * species[iSpec].acc_eddy;
+          dt * species[iSpec].acc_eddy;
     }
   }
-  
+
   calc_bulk_velocity();
 
   report.exit(function);

src/advance.cpp

@@ -51,14 +51,14 @@ int advance(Planets &planet,
 
   // ------------------------------------
   // Do advection first :
-  
+
   // Upper BCs requires the scale height to be calculated, so do that
   // first
-  
+
   neutrals.calc_scale_height(gGrid);
   neutrals.set_bcs(gGrid, time, indices);
   neutrals.advect_vertical(gGrid, time);
-  
+
   // ------------------------------------
   // Calculate source terms next:
 
@@ -96,8 +96,8 @@ int advance(Planets &planet,
   calc_ion_collisions(neutrals, ions);
   calc_neutral_friction(neutrals);
 
-  neutrals.add_sources(time);  
-  
+  neutrals.add_sources(time);
+
   ions.calc_ion_temperature(neutrals, gGrid, time);
   ions.calc_electron_temperature(neutrals, gGrid);
 

src/calc_ion_drift.cpp

@@ -78,7 +78,7 @@ void Ions::calc_ion_drift(Neutrals neutrals,
   int64_t nZ = grid.get_nZ();
 
   set_floor();
-  
+
   report.print(5, "going into calc_efield");
   calc_efield(grid);
 
@@ -95,7 +95,7 @@ void Ions::calc_ion_drift(Neutrals neutrals,
   std::vector<arma_cube> grad_Pi_plus_Pe;
   arma_cube rho, rho_nuin, nuin_sum, Nie, sum_rho;
   arma_cube top, bottom;
-  
+
   nuin_sum.set_size(nX, nY, nZ);
   nuin_sum.zeros();
 
@@ -128,7 +128,7 @@ void Ions::calc_ion_drift(Neutrals neutrals,
       // Want actual gravity for 3rd dim
       for (iDim = 0; iDim < 3; iDim ++)
         gravity_vcgc[iDim] = species[iIon].mass *
-	  grid.gravity_vcgc[iDim] % species[iIon].density_scgc;
+                             grid.gravity_vcgc[iDim] % species[iIon].density_scgc;
 
       // Neutral Wind Forcing:
       report.print(5, "neutral winds");
@@ -170,17 +170,17 @@ void Ions::calc_ion_drift(Neutrals neutrals,
 
         a_x_b = cross_product(a_perp, grid.bfield_vcgc);
 
-	// With floats, this can become 0, which then makes the
-	// velocity a nan, so the clamp ensures that the bottom is not 0
-	bottom =
-	  rho_nuin % rho_nuin +
-	  Nie % Nie % grid.bfield_mag_scgc % grid.bfield_mag_scgc;
-	bottom.clamp(1e-32, 1e32);
-	
+        // With floats, this can become 0, which then makes the
+        // velocity a nan, so the clamp ensures that the bottom is not 0
+        bottom =
+          rho_nuin % rho_nuin +
+          Nie % Nie % grid.bfield_mag_scgc % grid.bfield_mag_scgc;
+        bottom.clamp(1e-32, 1e32);
+
         for (int64_t iComp = 0; iComp < 3; iComp++) {
-	  top = rho_nuin % a_perp[iComp] + Nie % a_x_b[iComp];
-	  species[iIon].perp_velocity_vcgc[iComp] = top / bottom;
-	}
+          top = rho_nuin % a_perp[iComp] + Nie % a_x_b[iComp];
+          species[iIon].perp_velocity_vcgc[iComp] = top / bottom;
+        }
       } else {
         // No Planetary Magnetic field
         for (int64_t iComp = 0; iComp < 3; iComp++) {

src/calc_neutral_derived.cpp

@@ -125,12 +125,14 @@ void Neutrals::calc_bulk_velocity() {
 
   for (int64_t iDir = 0; iDir < 3; iDir++) {
     velocity_vcgc[iDir].zeros();
+
     for (int64_t iSpecies = 0; iSpecies < nSpecies; iSpecies++) {
       velocity_vcgc[iDir] = velocity_vcgc[iDir] +
-        species[iSpecies].mass *
-        species[iSpecies].density_scgc %
-        species[iSpecies].velocity_vcgc[iDir];
+                            species[iSpecies].mass *
+                            species[iSpecies].density_scgc %
+                            species[iSpecies].velocity_vcgc[iDir];
     }
+
     velocity_vcgc[iDir] = velocity_vcgc[iDir] / rho_scgc;
   }
 

src/inputs.cpp

@@ -696,26 +696,25 @@ json Inputs::get_boundary_condition_types() {
 std::string Inputs::get_advection_neutrals_vertical() {
 
   std::string value = "none";
-  
+
   if (settings.contains("Advection"))
     if (settings["Advection"].contains("Neutrals"))
       if (settings["Advection"]["Neutrals"].contains("Vertical"))
-	value = settings["Advection"]["Neutrals"]["Vertical"];
+        value = settings["Advection"]["Neutrals"]["Vertical"];
       else {
-	std::cout << "Error trying to get inputs:\n";
-	std::cout << "  settings['Advection']['Neutrals']['Vertical']\n";
-      }
-    else {
+        std::cout << "Error trying to get inputs:\n";
+        std::cout << "  settings['Advection']['Neutrals']['Vertical']\n";
+      } else {
       std::cout << "Error trying to get inputs:\n";
       std::cout << "  settings['Advection']['Neutrals']\n";
-    }
-  else {
+    } else {
     std::cout << "Error trying to get inputs:\n";
     std::cout << "  settings['Advection']\n";
   }
+
   return value;
 }
-  
+
 
 // --------------------------------------------------------------------------
 // check to see if class is ok

src/ions.cpp

@@ -43,7 +43,7 @@ Ions::species_chars Ions::create_species(Grid grid) {
 
   // The collision frequencies need the neutrals, so those are
   // initialized in init_ion_temperature.
-  
+
   return tmp;
 }
 
@@ -87,8 +87,10 @@ Ions::Ions(Grid grid, Planets planet) {
   density_scgc.set_size(nLons, nLats, nAlts);
   density_scgc.ones();
   velocity_vcgc = make_cube_vector(nLons, nLats, nAlts, 3);
+
   for (int iDir = 0; iDir < 3; iDir++)
     velocity_vcgc[iDir].zeros();
+
   temperature_scgc.set_size(nLons, nLats, nAlts);
   temperature_scgc.fill(200.0);
   electron_temperature_scgc.set_size(nLons, nLats, nAlts);
@@ -170,7 +172,7 @@ void Ions::set_floor() {
   int iSpecies;
 
   for (iSpecies = 0; iSpecies < nSpecies; iSpecies++)
-    species[iSpecies].density_scgc.clamp(1.0,1e15);
+    species[iSpecies].density_scgc.clamp(1.0, 1e15);
 
   return;
 }

src/neutrals.cpp

@@ -29,11 +29,12 @@ Neutrals::species_chars Neutrals::create_species(Grid grid) {
   tmp.newDensity_scgc.set_size(nLons, nLats, nAlts);
   tmp.velocity_vcgc = make_cube_vector(nLons, nLats, nAlts, 3);
   tmp.newVelocity_vcgc = make_cube_vector(nLons, nLats, nAlts, 3);
+
   for (int iDir = 0; iDir < 3; iDir++) {
     tmp.velocity_vcgc[iDir].zeros();
     tmp.newVelocity_vcgc[iDir].zeros();
   }
-  
+
   tmp.chapman_scgc.set_size(nLons, nLats, nAlts);
   tmp.scale_height_scgc.set_size(nLons, nLats, nAlts);
   tmp.ionization_scgc.set_size(nLons, nLats, nAlts);
@@ -109,8 +110,10 @@ Neutrals::Neutrals(Grid grid,
   rho_scgc.set_size(nLons, nLats, nAlts);
   rho_scgc.ones();
   velocity_vcgc = make_cube_vector(nLons, nLats, nAlts, 3);
+
   for (int iDir = 0; iDir < 3; iDir++)
     velocity_vcgc[iDir].zeros();
+
   cMax_vcgc = make_cube_vector(nLons, nLats, nAlts, 3);
   mean_major_mass_scgc.set_size(nLons, nLats, nAlts);
   mean_major_mass_scgc.ones();
@@ -201,8 +204,8 @@ void Neutrals::fill_with_hydrostatic(int64_t iStart,
     // Integrate with hydrostatic equilibrium up:
     for (int iAlt = iStart; iAlt < iEnd; iAlt++) {
       species[iSpecies].density_scgc.slice(iAlt) =
-	temperature_scgc.slice(iAlt - 1) /
-	temperature_scgc.slice(iAlt) %
+        temperature_scgc.slice(iAlt - 1) /
+        temperature_scgc.slice(iAlt) %
         species[iSpecies].density_scgc.slice(iAlt - 1) %
         exp(-grid.dalt_lower_scgc.slice(iAlt) /
             species[iSpecies].scale_height_scgc.slice(iAlt));

src/neutrals_advect.cpp

@@ -12,7 +12,7 @@
 bool Neutrals::advect_vertical(Grid grid, Times time) {
 
   bool didWork = true;
-  
+
   std::string function = "Neutrals::advance_vertical";
   static int iFunction = -1;
   report.enter(function, iFunction);
@@ -24,10 +24,11 @@ bool Neutrals::advect_vertical(Grid grid, Times time) {
   else {
     std::cout << "Vertical solver not found!\n";
     std::cout << "  ==> Requested : "
-	      << input.get_advection_neutrals_vertical()
-	      << "\n";
+              << input.get_advection_neutrals_vertical()
+              << "\n";
     didWork = false;
   }
+
   report.exit(function);
   return didWork;
 }

src/neutrals_momentum_friction.cpp

@@ -93,30 +93,30 @@ void calc_neutral_friction(Neutrals &neutrals) {
   for (iDir = 0; iDir < 3; iDir++) {
     if (iDir < 2) {
       for (iSpecies = 0; iSpecies < neutrals.nSpecies; iSpecies++)
-	neutrals.species[iSpecies].acc_neutral_friction[iDir].zeros();
+        neutrals.species[iSpecies].acc_neutral_friction[iDir].zeros();
     } else {
-    
+
       for (iAlt = 0; iAlt < nZs; iAlt++) {
-	for (iLat = 0; iLat < nYs; iLat++) {
-	  for (iLon = 0; iLon < nXs; iLon++) {
-	    vels.zeros();
-
-	    //Put the old velocities into vels:
-	    for (iSpecies = 0; iSpecies < neutrals.nSpecies; iSpecies++)
-	      vels(iSpecies) =
-		neutrals.species[iSpecies].velocity_vcgc[iDir](iLon, iLat, iAlt);
-
-	    acc = neutral_friction_one_cell(iLon, iLat, iAlt, vels, neutrals);
-
-	    for (iSpecies = 0; iSpecies < neutrals.nSpecies; iSpecies++)
-	      neutrals.species[iSpecies].acc_neutral_friction[iDir](iLon, iLat, iAlt) =
-		acc(iSpecies);
-	  } // for long
-	} // for lat
+        for (iLat = 0; iLat < nYs; iLat++) {
+          for (iLon = 0; iLon < nXs; iLon++) {
+            vels.zeros();
+
+            //Put the old velocities into vels:
+            for (iSpecies = 0; iSpecies < neutrals.nSpecies; iSpecies++)
+              vels(iSpecies) =
+                neutrals.species[iSpecies].velocity_vcgc[iDir](iLon, iLat, iAlt);
+
+            acc = neutral_friction_one_cell(iLon, iLat, iAlt, vels, neutrals);
+
+            for (iSpecies = 0; iSpecies < neutrals.nSpecies; iSpecies++)
+              neutrals.species[iSpecies].acc_neutral_friction[iDir](iLon, iLat, iAlt) =
+                acc(iSpecies);
+          } // for long
+        } // for lat
       } // for alt
     } // if iDir
   } // for direction
-    
+
   report.exit(function);
   return;
 } //calc_neutral_friction

src/solver_vertical_rusanov.cpp

@@ -113,7 +113,7 @@ void calc_grad_and_diff_alts_rusanov(Grid &grid,
 
   outDiff.zeros();
   outGrad.zeros();
-  
+
   report.print(3, "before facevalues");
 
   calc_facevalues_alts_rusanov(grid, inVar, varLeft, varRight);
@@ -279,8 +279,8 @@ void Neutrals::solver_vertical_rusanov(Grid grid,
         - dt * (species[iSpecies].velocity_vcgc[2] % gradVertVel_s[iSpecies]
                 - v2or
                 + 0.1 * (temperature_scgc % gradLogN_s[iSpecies] * cKB / mass
-			 + gradTemp * cKB / mass
-			 + abs(grid.gravity_vcgc[2])))
+                         + gradTemp * cKB / mass
+                         + abs(grid.gravity_vcgc[2])))
         + dt * diffVertVel_s[iSpecies];
     } else {
       species[iSpecies].newVelocity_vcgc[2].zeros();
@@ -326,13 +326,13 @@ void Neutrals::solver_vertical_rusanov(Grid grid,
         for (iSpecies = 0; iSpecies < nSpecies; iSpecies++) {
           if (species[iSpecies].DoAdvect) {
             species[iSpecies].density_scgc(iX, iY, iZ) =
-	      species[iSpecies].newDensity_scgc(iX, iY, iZ);
+              species[iSpecies].newDensity_scgc(iX, iY, iZ);
             species[iSpecies].velocity_vcgc[2](iX, iY, iZ) =
               species[iSpecies].newVelocity_vcgc[2](iX, iY, iZ);
           } else {
             // assign bulk vertical velocity to the non-advected species:
             species[iSpecies].velocity_vcgc[2](iX, iY, iZ) =
-	      velocity_vcgc[2](iX, iY, iZ);
+              velocity_vcgc[2](iX, iY, iZ);
           }
         }
       }

src/time.cpp

@@ -109,7 +109,7 @@ void Times::calc_dt(precision_t dtNeutral,
   dt = end - current;
 
   double cfl = 0.5;
-  
+
   if (cfl * dtNeutral < dt)
     dt = cfl * dtNeutral;