Allow components to call for creation of sub components

CMakeLists.txt

@@ -73,6 +73,7 @@ set(HERMES_SOURCES
     src/evolve_energy.cxx
     src/evolve_pressure.cxx
     src/evolve_momentum.cxx
+    src/guarded_options.cxx
     src/isothermal.cxx
     src/quasineutral.cxx
     src/diamagnetic_drift.cxx
@@ -93,6 +94,7 @@ set(HERMES_SOURCES
     src/noflow_boundary.cxx
     src/neutral_parallel_diffusion.cxx
     src/neutral_boundary.cxx
+    src/permissions.cxx
     src/polarisation_drift.cxx
     src/solkit_neutral_parallel_diffusion.cxx
     src/hydrogen_charge_exchange.cxx
@@ -113,6 +115,7 @@ set(HERMES_SOURCES
     include/anomalous_diffusion.hxx
     include/classical_diffusion.hxx
     include/binormal_stpm.hxx
+    include/braginskii_closure.hxx
     include/braginskii_collisions.hxx
     include/braginskii_conduction.hxx
     include/braginskii_electron_viscosity.hxx
@@ -133,6 +136,7 @@ set(HERMES_SOURCES
     include/fixed_density.hxx
     include/fixed_fraction_ions.hxx
     include/fixed_velocity.hxx
+    include/guarded_options.hxx
     include/neutral_full_velocity.hxx
     include/hermes_utils.hxx
     include/hydrogen_charge_exchange.hxx
@@ -144,6 +148,7 @@ set(HERMES_SOURCES
     include/neutral_parallel_diffusion.hxx
     include/solkit_neutral_parallel_diffusion.hxx
     include/noflow_boundary.hxx
+    include/permissions.hxx
     include/polarisation_drift.hxx
     include/quasineutral.hxx
     include/reaction.hxx
@@ -279,6 +284,7 @@ if(HERMES_TESTS)
   hermes_add_integrated_test(alfven-wave)
   hermes_add_integrated_test(collfreq-braginskii-afn)
   hermes_add_integrated_test(collfreq-multispecies)
+  hermes_add_integrated_test(component-order)
 
   # Unit tests
   option(HERMES_UNIT_TESTS "Build the unit tests" ON)

docs/sphinx/boundary_conditions.rst

@@ -250,7 +250,7 @@ The boundary fluxes might be set by sheath boundary conditions,
 which potentially depend on the density and temperature of all species.
 Recycling therefore can't be calculated until all species boundary conditions
 have been set. It is therefore expected that this component is a top-level
-component (i.e. in the `Hermes` section) which comes after boundary conditions are set.
+component (i.e. in the `Hermes` section).
 
 Recycling has been implemented at the target, the SOL edge and the PFR edge.
 Each is off by default and must be activated with a separate flag. Each can be 
@@ -620,4 +620,4 @@ Note that if you have the density controller enabled, it will work to counteract
    function = 0.01
    source = Pe:source
    source_time_dependent = true
-   source_prefactor = Pe:source_prefactor
+   source_prefactor = Pe:source_prefactor

docs/sphinx/closure.rst

@@ -39,7 +39,12 @@ The parallel projection of diffusion from the wall in 1D
 is captured in the :ref:`neutral_parallel_diffusion` top-level component, while 
 both parallel Braginskii transport and perpendicular pressure-diffusion for 2D/3D 
 are captured in the :ref:`neutral_mixed` species-level component. 
-
+
+A user can automatically activate all of these components at once
+using the `BraginskiiClosure` component.
+
+.. doxygenclass:: BraginskiiClosure
+   :members:
 
 
 Collision frequency selection
@@ -262,8 +267,7 @@ Input
 
 This top-level component calculates the frictional forces between each
 pair of species for which collisional frequencies have been calculated
-(see :ref:`Braginskii Collisions`). As such, it must be run after
-`braginskii_collisions`. If the option `frictional_heating` is
+(see `Braginskii Collisions component`_). If the option `frictional_heating` is
 enabled then it will also calculate the energy source arising from
 friction.
 
@@ -346,8 +350,8 @@ Braginskii Heat Exchange
 Input
 -----
 This top-level component calculates the heat exchange between species
-due to collisions (see :ref:`Braginskii Collisions`). As such, it must be run after
-`braginskii_collisions`. There are no configurations for this component.
+due to collisions (see `Braginskii Collisions component`_). There are no
+configurations for this component.
 
 Theory
 ------