Merge pull request #436 from ammarhakim/moment_source_rewrite_braginskii

Adding back in all the Braginskii work

apps/gkyl_moment.h

@@ -2,6 +2,7 @@
 
 #include <gkyl_app.h>
 #include <gkyl_comm.h>
+#include <gkyl_moment_braginskii.h>
 #include <gkyl_mp_scheme.h>
 #include <gkyl_util.h>
 #include <gkyl_wave_prop.h>
@@ -18,6 +19,7 @@ struct gkyl_moment_species {
   enum gkyl_wave_limiter limiter; // limiter to use
   enum gkyl_wave_split_type split_type; // edge splitting to use
 
+  enum gkyl_braginskii_type type_brag; // which Braginskii equations
   bool has_grad_closure; // has gradient-based closure (only for 10 moment) 
 
   bool has_friction; // Run with frictional sources.
@@ -159,6 +161,9 @@ struct gkyl_moment {
 
   bool has_nT_sources;
 
+  bool has_braginskii; // has Braginskii transport
+  double coll_fac; // multiplicative collisionality factor for Braginskii  
+
   // this should not be set by typical user-facing code but only by
   // higher-level drivers
   bool has_low_inp; // should one use low-level inputs?

apps/gkyl_moment_priv.h

@@ -24,6 +24,7 @@
 #include <gkyl_kep_scheme.h>
 #include <gkyl_mhd_src.h>
 #include <gkyl_moment.h>
+#include <gkyl_moment_braginskii.h>
 #include <gkyl_moment_em_coupling.h>
 #include <gkyl_mp_scheme.h>
 #include <gkyl_range.h>
@@ -34,6 +35,8 @@
 #include <gkyl_wave_geom.h>
 #include <gkyl_wave_prop.h>
 #include <gkyl_wv_apply_bc.h>
+#include <gkyl_wv_euler.h>
+#include <gkyl_wv_iso_euler.h>
 #include <gkyl_wv_maxwell.h>
 #include <gkyl_wv_mhd.h>
 #include <gkyl_wv_ten_moment.h>
@@ -46,6 +49,7 @@ struct moment_species {
 
   double k0; // closure parameter (default is 0.0, used by 10 moment)
   bool has_grad_closure; // has gradient-based closure (only for 10 moment)
+  enum gkyl_braginskii_type type_brag; // which Braginskii equations
 
   bool has_friction; // Run with frictional sources.
   bool use_explicit_friction; // Use an explicit (SSP-RK3) solver for integrating frictional sources.
@@ -178,16 +182,19 @@ struct moment_field {
 
 // Source data
 struct moment_coupling {
-// grid for braginskii variables (braginskii variables located at cell nodes)  
+  // grid for braginskii variables (braginskii variables located at cell nodes)  
   struct gkyl_rect_grid non_ideal_grid;
- // local, local-ext ranges for braginskii variables (loop over nodes)  
+  // local, local-ext ranges for braginskii variables (loop over nodes)  
   struct gkyl_range non_ideal_local, non_ideal_local_ext;
 
- // Gradient-based closure solver (if present)  
-  gkyl_ten_moment_grad_closure *grad_closure_slvr[GKYL_MAX_SPECIES];
- // array for stable time-step from non-ideal terms  
+  // Gradient-based closure solver (if present)  
+  struct gkyl_ten_moment_grad_closure *grad_closure_slvr[GKYL_MAX_SPECIES];
+  // Braginskii solver (if present)
+  struct gkyl_moment_braginskii *brag_slvr; 
+
+  // array for stable time-step from non-ideal terms  
   struct gkyl_array *non_ideal_cflrate[GKYL_MAX_SPECIES];
- // array for non-ideal variables (heat-flux tensor)  
+  // array for non-ideal variables (heat-flux tensor)  
   struct gkyl_array *non_ideal_vars[GKYL_MAX_SPECIES];
   // array for storing RHS of each species from non-ideal term updates (gradient-based closure)
   struct gkyl_array  *pr_rhs[GKYL_MAX_SPECIES];
@@ -215,6 +222,9 @@ struct gkyl_moment_app {
  // should shock-hybrid scheme be used when using KEP?  
   bool use_hybrid_flux_kep;
 
+  bool has_braginskii; // has Braginskii transport
+  double coll_fac; // multiplicative collisionality factor for Braginskii  
+
   int num_periodic_dir; // number of periodic directions
   int periodic_dirs[3]; // list of periodic directions
   int nghost[3]; // number of ghost-cells in each direction

apps/mom_coupling.c

@@ -134,6 +134,36 @@ moment_coupling_init(const struct gkyl_moment_app *app, struct moment_coupling *
       src->grad_closure_slvr[i] = gkyl_ten_moment_grad_closure_new(grad_closure_inp);
     }
   }
+
+  // check if braginskii terms are present
+  if (app->has_braginskii) {
+    struct gkyl_moment_braginskii_inp brag_inp = {
+      .grid = &app->grid,
+      .nfluids = app->num_species,
+      .epsilon0 = app->field.epsilon0,
+      // Check for multiplicative collisionality factor, default is 1.0
+      .coll_fac = app->coll_fac == 0 ? 1.0 : app->coll_fac,
+    };
+    for (int i=0; i<app->num_species; ++i) {
+      // Braginskii coefficients depend on pressure and coefficient to obtain
+      // pressure is different for different equation systems (gasGamma, vt, Tr(P))
+      double p_fac = 1.0;
+      if (app->species[i].eqn_type == GKYL_EQN_EULER) {
+        p_fac =  gkyl_wv_euler_gas_gamma(app->species[i].equation);
+      }
+      else if (app->species[i].eqn_type == GKYL_EQN_ISO_EULER) {
+        p_fac =  gkyl_wv_iso_euler_vt(app->species[i].equation);
+      }
+      brag_inp.param[i] = (struct gkyl_moment_braginskii_data) {
+        .type_eqn = app->species[i].eqn_type,
+        .type_brag = app->species[i].type_brag,
+        .charge = app->species[i].charge,
+        .mass = app->species[i].mass,
+        .p_fac = p_fac,
+      };
+    }
+    src->brag_slvr = gkyl_moment_braginskii_new(brag_inp);
+  }
 }
 
 // update sources: 'nstrang' is 0 for the first Strang step and 1 for
@@ -165,6 +195,13 @@ moment_coupling_update(gkyl_moment_app *app, struct moment_coupling *src,
     }
   }
 
+  if (app->has_braginskii) {
+    gkyl_moment_braginskii_advance(src->brag_slvr,
+      src->non_ideal_local_ext, app->local,
+      fluids, app->field.f[sidx[nstrang]],
+      src->non_ideal_cflrate, src->non_ideal_vars, src->pr_rhs);
+  }
+
   if (app->field.proj_app_current)
     gkyl_fv_proj_advance(app->field.proj_app_current, tcurr, &app->local, app->field.app_current);
   if ((app->field.proj_app_current) && (app->field.use_explicit_em_coupling)){

apps/mom_species.c

@@ -22,6 +22,10 @@ moment_species_init(const struct gkyl_moment *mom, const struct gkyl_moment_spec
   sp->k0 = mom_sp->equation->type == GKYL_EQN_TEN_MOMENT ? gkyl_wv_ten_moment_k0(mom_sp->equation) : 0.0;
   // check if we are running with gradient-based closure
   sp->has_grad_closure = mom_sp->has_grad_closure == 0 ? 0 : mom_sp->has_grad_closure;
+  // check if we are running with Braginskii transport and fetch Braginskii type
+  if (app->has_braginskii) {
+    sp->type_brag = mom_sp->type_brag;
+  }
 
   if (mom_sp->has_friction) {
     sp->has_friction = true;

apps/moment.c

@@ -129,6 +129,10 @@ gkyl_moment_app_new(struct gkyl_moment *mom)
     moment_field_init(mom, &mom->field, app, &app->field);
   }
 
+  // Are we running with Braginskii transport?
+  app->has_braginskii = mom->has_braginskii;
+  app->coll_fac = mom->coll_fac;
+
   int ns = app->num_species = mom->num_species;
   // allocate space to store species objects
   app->species = ns>0 ? gkyl_malloc(sizeof(struct moment_species[ns])) : 0;