Fix for when a new level is created (#98)

Also correct incflo.H include guard, a typo and a couple outdated
comments.

.github/workflows/docs.yml

@@ -31,5 +31,5 @@ jobs:
           ssh-key: ${{ secrets.DEPLOY_KEY }}
           branch: gh-pages # The branch the action should deploy to.
           folder: Docs/sphinx_documentation/build/html # The folder the action should deploy.
-          target_folder: docs_html # The folder the action should deploy to.
+          target-folder: docs_html # The folder the action should deploy to.
           clean: false # Do not remove existing files from the deploy target.

src/incflo.H

@@ -1,4 +1,5 @@
 #ifndef INCFLO_H_
+#define INCFLO_H_
 
 #include <AMReX_AmrCore.H>
 #include <AMReX_MultiFabUtil.H>

src/incflo_apply_predictor.cpp

@@ -11,7 +11,10 @@ using namespace amrex;
 //      else
 //          conv_u  = - del dot (rho u u)
 //      conv_r  = - div( u rho  )
-//      conv_t  = - div( u trac )
+//      if (m_iconserv_tracer) then
+//          conv_t  = - div( u trac )
+//      else
+//          conv_t  = - u dot grad trac
 //      eta_old     = visosity at m_cur_time
 //      if (m_diff_type == DiffusionType::Explicit)
 //         divtau _old = div( eta ( (grad u) + (grad u)^T ) ) / rho^n
@@ -168,7 +171,6 @@ void incflo::ApplyPredictor (bool incremental_projection)
     //      Compute the explicit advective terms R_u^(n+1/2), R_s^(n+1/2) and R_t^(n+1/2)
     // if (advection_type == "MOL"                )
     //      Compute the explicit advective terms R_u^n      , R_s^n       and R_t^n
-    // Note that "get_conv_tracer_old" returns div(rho u tracer)
     // *************************************************************************************
     compute_convective_term(get_conv_velocity_old(), get_conv_density_old(), get_conv_tracer_old(),
                             get_velocity_old_const(), get_density_old_const(), get_tracer_old_const(),

src/incflo_regrid.cpp

@@ -43,18 +43,17 @@ void incflo::MakeNewLevelFromCoarse (int lev,
     m_leveldata[lev] = std::move(new_leveldata);
     m_factory[lev] = std::move(new_fact);
 
-    //make_mixedBC_mask(lev, ba, dm);
-
     m_diffusion_tensor_op.reset();
     m_diffusion_scalar_op.reset();
 
+    // Note: finest_level has not yet been updated and so we use lev
 #ifdef AMREX_USE_EB
-    macproj = std::make_unique<Hydro::MacProjector>(Geom(0,finest_level),
+    macproj = std::make_unique<Hydro::MacProjector>(Geom(0,lev),
                       MLMG::Location::FaceCentroid,  // Location of mac_vec
                       MLMG::Location::FaceCentroid,  // Location of beta
                       MLMG::Location::CellCenter  ); // Location of solution variable phi
 #else
-    macproj = std::make_unique<Hydro::MacProjector>(Geom(0,finest_level));
+    macproj = std::make_unique<Hydro::MacProjector>(Geom(0,lev));
 #endif
 }