add excitation to the hydrogen radiation sink term - copied from SD1D

.vscode/c_cpp_properties.json

@@ -0,0 +1,17 @@
+{
+    "configurations": [
+        {
+            "name": "Linux",
+            "includePath": [
+                "${workspaceFolder}/**",
+                "/lus/cls01095/work/e281/e281/hm1234/BOUT/dec21/BOUT-dev/**"
+            ],
+            "defines": [],
+            "compilerPath": "/opt/gcc/10.1.0/bin/gcc",
+            "cStandard": "gnu17",
+            "cppStandard": "gnu++14",
+            "intelliSenseMode": "linux-gcc-x64"
+        }
+    ],
+    "version": 4
+}

include/hermes-2.hxx

@@ -48,6 +48,7 @@ private:
   // Equilibrium current
   Field2D Jpar0;
 
+  BoutReal nelim_floor; // Global density floor
   BoutReal nesheath_floor; // Density floor used in sheath boundary conditions
 
   // Evolving variables
@@ -142,6 +143,7 @@ private:
   bool sheath_closure; // Sheath closure sink on vorticity (if sinks = true)
   bool drift_wave;     // Drift-wave closure (if sinks=true)
 
+  bool slab_radial_buffers; // an alternatice radial buffer region for use in slab geometry
   bool radial_buffers; // Radial buffer regions
   int radial_inner_width; // Number of points in the inner radial buffer
   int radial_outer_width; // Number of points in the outer radial buffer
@@ -181,14 +183,16 @@ private:
   BoutReal numdiff, hyper, hyperpar; ///< Numerical dissipation
   int low_pass_z; // Fourier filter in Z 
   BoutReal z_hyper_viscos, x_hyper_viscos, y_hyper_viscos; // 4th-order derivatives
-  bool low_n_diffuse; // Diffusion in parallel direction at low density
-  bool low_n_diffuse_perp; // Diffusion in perpendicular direction at low density
+  BoutReal low_n_diffuse; // Diffusion in parallel direction at low density
+  BoutReal low_n_diffuse_perp; // Diffusion in perpendicular direction at low density
   BoutReal ne_hyper_z, pe_hyper_z; // Hyper-diffusion
+  BoutReal nvi_hyper_z, vepsi_hyper_z; // hyper-diffusion on ion terms
   BoutReal scale_num_cs; // Scale numerical sound speed
   BoutReal floor_num_cs; // Apply a floor to the numerical sound speed
   bool vepsi_dissipation; // Dissipation term in VePsi equation
   bool vort_dissipation; // Dissipation term in Vorticity equation
-  bool phi_dissipation; // Dissipation term in Vorticity equation, depending on phi
+  BoutReal phi_dissipation; // Dissipation term in Vorticity equation, depending on phi
+  BoutReal delp2_dissipation; // Dissipation using delp2
 
   // Sources and profiles
 
@@ -222,6 +226,7 @@ private:
 
   // Curvature, Grad-B drift
   Vector3D Curlb_B; // Curl(b/B)
+  bool revCurlb_B; // Reverse direction of Curl(b/B) vector
 
   // Perturbed parallel gradient operators
   const Field3D Grad_parP(const Field3D &f);

include/mixed.hxx

@@ -33,6 +33,8 @@ private:
   Field3D Pnlim;  // Limited pressure, used to calculate pressure-driven diffusive flows
   Field3D Vn;
   Field3D Dnn;
+
+  Field3D Riz, Rrc, Rcx, Rex;
 
   bool sheath_ydown, sheath_yup;
 

include/neutral-model.hxx

@@ -26,6 +26,7 @@ public:
 
     // Options for calculating rates
     OPTION(options, Eionize, 30); // Energy loss per ionisation [eV]
+    OPTION(options, h_excitation, true); // Add to plasma radiation sink
   }
   virtual ~NeutralModel() {}
 
@@ -74,11 +75,13 @@ protected:
   UpdatedRadiatedPower hydrogen; // Atomic rates (H.Willett)
 
   BoutReal Eionize;   // Energy loss per ionisation [eV]
+
+  bool h_excitation; // add excitation energy to the hydrogen radiation energy sink
 
   void neutral_rates(const Field3D &Ne, const Field3D &Te, const Field3D &Ti, const Field3D &Vi,    // Plasma quantities
                      const Field3D &Nn, const Field3D &Tn, const Field3D &Vnpar, // Neutral gas
                      Field3D &S, Field3D &F, Field3D &Qi, Field3D &R,  // Transfer rates
-                     Field3D &Riz, Field3D &Rrc, Field3D &Rcx);        // Rates
+                     Field3D &Riz, Field3D &Rrc, Field3D &Rcx, Field3D &Rex);        // Rates
 
 private:
   NeutralModel();

include/revision.hxx

@@ -0,0 +1,26 @@
+/// Information about the version of Hermes
+///
+/// The build system will update this file on every commit, which may
+/// result in files that include it getting rebuilt. Therefore it
+/// should be included in as few places as possible
+
+#ifndef HERMES_REVISION_H
+#define HERMES_REVISION_H
+
+namespace hermes {
+namespace version {
+/// The git commit hash
+#ifndef HERMES_REVISION
+constexpr auto revision = "@HERMES_REVISION@";
+#else
+// Stringify value passed at compile time
+#define BUILDFLAG1_(x) #x
+#define BUILDFLAG(x) BUILDFLAG1_(x)
+constexpr auto revision = BUILDFLAG(HERMES_REVISION);
+#undef BUILDFLAG1
+#undef BUILDFLAG
+#endif
+} // namespace version
+} // namespace hermes
+
+#endif // HERMES_REVISION_H

src/full-velocity.cxx

@@ -324,10 +324,10 @@ void FullVelocity::update(const Field3D &Ne, const Field3D &Te,
   /////////////////////////////////////////////////////
   // Atomic processes
 
-  Field3D Riz, Rrc, Rcx;
-  neutral_rates(Ne, Te, Ti, Vi, Nn, Tn, Vnpar, S, F, Qi, Rp, Riz, Rrc, Rcx);
+  Field3D Riz, Rrc, Rcx, Rex;
+  neutral_rates(Ne, Te, Ti, Vi, Nn, Tn, Vnpar, S, F, Qi, Rp, Riz, Rrc, Rcx, Rex);
 
-  Fperp = Rrc + Rcx; // Friction for vorticity
+  Fperp = Rrc + Rcx + Rex; // Friction for vorticity
 
   // Loss of momentum in the X and Z directions
   ddt(Vn2D).x -= (DC(Rcx) + DC(Riz)) * Vn2D.x / Nn2D_floor;