Hydro/MHD C++ Infrastructure

[This page is under development]

In this section we discuss some of the C++ infrastructure provided in the Enzo Layer that can be optionally used to implement other hydro/MHD methods. The infrastructure was used to implement other the VL + CT MHD solver.

Note: Currently, barotropic equations of state are not yet implemented within the infrastucture. However they are mentioned throughout this guide and slots have been explicitly left open for them to be implemented within the framework.

Note: Currently brief summaries of the interfaces of each of the objects are provided below. More detailed descriptions are provided in the header files using doxygen documentation. If we end up producing reference documentation from doxygen (via breathe), then the interface summaries should be reduced or deleted.

Shorthand Terms

We briefly define a few terms that are used throughout the documentation and codebase

Integration/Primitive Quantities

Throughout this guide and the relevant sections of the codebase, we categorize quantities as integration quantities and primitives.

The integration quantities are the cell-centered quantities that Enzo-E, as a whole, uses to describe the state of the fluid. In other words, these are the hydro/MHD quantities that Enzo-E expects to be integrated from one time-step to the next. The integration quantities include all passive scalars in their “conserved” form (i.e. as densities). All integration quantities can basically be subcategorized as either “conserved” or “specific” (a specific quantity like velocity that becomes conserved after multiplication by density). In cases using the dual energy formalism, we treat the specific internal energy as an integration quantity even though the internal energy density is not technically conserved (it requires source terms).

The primitive quantities follow the normal textbook definition. We use the primitives internally within the hydro/MHD solver for reconstruction. The primitives include all passive scalars in their “specific” form (i.e. as mass fractions). Note that some quantities (like density or velocity) are categorized as both an integration quantity and a primitive.

To provide a more concrete example, we categorize the quantities related to an ideal, adiabatic gas:

• density - integration and primitive

• velocity - integration and primitive

• pressure - only primitive

• (specific) total energy - only integration

• magnetic field - integration and primitive

If using the dual energy formalism, we would categorize the (specific) internal energy as an integration quantity. As of now, there wouldn’t be a primitive counterpart to the internal energy since it can be computed from the reconstructed density and pressure.

stale depth

To help simplify the implementation of several operations, we introduce the concept of “stale depth”. At the start of a time-step, there are never any “stale” values (“stale depth” is zero). However, every time the flux divergence get’s added to any quantities, the outermost layer of up-to-date quantities (in the ghost zone) becomes invalid; this happens because the fluxes on the exterior faces of that layer are not accurately known. We refer to these invalid values as “stale” and say that the stale depth increased by 1. The stale depth can also be incremented by other operations (e.g. piecewise linear reconstruction). At the end of a time-step, the stale depth should be equal to or less than the ghost depth so that the all of the “stale” values will be refreshed (resetting the “stale depth” to zero).

We formally define “stale depth” as the number of the layers of the outermost field entries that include “stale” values (for cell-centered fields this is the number of cells from the edge that include stale values). For a given stale depth:

• A face-centered field that has values on the exterior of a mesh block will always have one more unstaled value along the axis of face-centering than a cell-centered field.

• A face-centered field that doesn’t have values on the exterior of a mesh block will always have one less unstaled value along the axis of face-centering than a cell-centered field.

The introduction of this formalism has 2 key benefits:

1. Simplifies calculation of the required ghost depth.

2. When used alongside CelloArray, it drastically simplifies the determination of which indices to iterate over. The EnzoFieldArrayFactory can take the stale depth as an argument in its constructor and then all arrays that an instance builds will have the stale values clipped off. This allows the bounds of for-loops to be written as though the only reconstruction algorithm is nearest-neighbor interpolation and as though there never any preceeding partial timesteps.

Finally, for each reconstruction algorithm we define a staling rate. This specifies the amount that the stale depth increases each time values are updated over a (partial) timestep using the algorithm. This is subdivided into

1. “immediate staling rate,” which species the amount by whch the stale-depth increases immediately after reconstruction (e.g. this is 0 for nearest-neighbor interpolation and 1 for piecewise-linear interpolation).

2. “delayed staling rate,” which specifies the amount by which the stale depth increase after adding the flux divergence (e.g. 1 for both nearest-neighbor and piecewise linear interpolation).

Centered Field Registry

The Hydro/MHD infrastructure helped motivate the creation of EnzoCenteredFieldRegistry, to encapsulate a static (at runtime) registry of all known fields used by the Enzo section of the codebase and track some basic meta-data about the fields. Although it’s functionallity is presently limited, the EnzoCenteredFieldRegistry has the potential to be a general purpose tool that can be used for other purposes in the Enzo layer of the codebase.

The idea is to maintain a list of all quantities, represented by cell-centered fields, that are used by Enzo in the FIELD_TABLE macro. For each quantity, the table currently tracks its name, whether its fundamentally a scalar or vector quantity, if the quantity can be classified as “conserved”, “specific”, or “other”, and whether or not there is any circumstance in the codebase where the quantity is “actively” advected. An entry about a scalar quantity registers a field of the same name. An entry for a vector quantity registers 3 fields with the names "{qname}_x", "{qname}_y", "{qname}_z", where {qname} is the name of the quantity (e.g. the row for the “velocity” quantity registers the "velocity_x", "velocity_y", and "velocity_z" fields).

At present, the registry currently provides operations:

• to access quantity properties registered in FIELD_TABLE at runtime

• to provide a list of known groups that can be used in the input file to identify fields as passively advected scalars (as of now, the only such group is "color").

General Design

Overview

The hydrodynamic/MHD C++ toolkit can be summarized as a series of classes that encapsulate various operations that performed by hydrodynamic/MHD integrators. In most cases an abstract base class exists to provide the interface for each operation. The main operation classes include:

• EnzoEquationOfState - encapsulates many of the operations related to the fluid’s equation of state (e.g. computing pressure, converting the integration quantities or primitives)

• EnzoReconstructor - encapsulates interpolation algorithms to reconstruct left/right interface states of cell-centered values

• EnzoRiemann - encapsulates various Rimann Solver algorithms

• EnzoIntegrationQuanUpdate - encapsulates the operation of updating integration quantities after a (partial) time-step.

• EnzoBfieldMethod - encapsulates operations related to integrating magnetic fields that are not performed by the other operation classes. For example, a subclass exists for supporting Constrained Transport.

Each of these operation classes are fairly modular (to allow for selective usage of the frame work components). However, all of the classes require that an instance of EnzoEquationOfState get’s passed. The operation classes are also provided with PUP methods to allow for easy serialization alongside the Method class that makes use of them.

Each of the operation classes are designed to be configured upon initialization. The instances can then be used multiple times per time-step (along multiple dimensions if the operation is directional) and in other time-steps. Lists (excluding passive scalars) of the expected primitives and integration keys are respectively registered during the construction of EnzoReconstructor and EnzoIntegrationQuanUpdate. These keys must each share a name with the registered quantities in FIELD_TABLE. In contrast, configuration of EnzoRiemann, is less flexible and instances actually specify the non-passive integration quantities and non-passive primitives that they require. This difference exists because the operations encapsulated by EnzoReconstructor and EnzoIntegrationQuanUpdate can be applied to individual quantities in a far more independent manner.

Because all fields storing passively advected scalars are not necessarily known when initializing a hydro/MHD integrator (i.e. they could be initialized by a different Method or an initializer), the passively advected scalars don’t need to be registered when constructing these classes. Instead, a std::vector<std::string> specifying the names of the passive scalars is often passed to the method(s) of the class that perform(s) the encapsulated operation.

The implementation of these operation classes aims to avoid the traditional approach in which field data is directly accessed from a large array using macros or globally defined unscoped enums that maps quantity component names to indices. This traditional approach makes the introuduction of optional fields that are related to active advection somewhat difficult (e.g. cosmic ray energy/fluxes, internal energy for dual energy formalism, phi for dedner divergence cleaning). Instead, our toolkit largely operates on maps/dictionaries containing EFlt3DArray instances (stored in EnzoEFltArrayMap).

Use of EnzoEFltArrayMap

The basic unit that get’s operated on by these operation classes are instances of the EnzoEFltArrayMap class. As the name may suggest, these classes serve as a map/dictionary of instances of EFlt3DArray (or equivalently, instances of CelloArray<enzo_float,3>). For more details about how to use EnzoEFltArrayMap, see EnzoEFltArrayMap

In the context of this toolkit, the keys of an EnzoEFltArrayMap are usually the names of a scalar quantity (like "density") or component of a vector quantity (like "velocity_x"). Each key is paired with an instance of EFlt3DArray that stores associated data. To simplify logic, arrays are not aliased between separate maps. Below, we provide a description of the main uses of EnzoEFltArrayMap by the provided operation classes:

1. Map of cell-centered integration quantities.

   • This has keys named for all integration scalar quantities and components of integration vector quantities. The associated arrays hold the values of the cell-centered quantities at a given time.

   • This also contains key-value pairs for passively advected scalars. In this context, the passive scalars are stored in “conserved” form.

   • In a predictor-corrector scheme (like VL+CT), we might have multiple maps used to store values at different partial timesteps.

2. Map of cell-centered primitive quantities.

   • This map is used to temporarily store the cell-centered primitive quantities for use in reconstruction.

   • This also contains key-value pairs for passively advected scalars. In this context, the passive scalars are stored in “specific” form.

   • Quantities in both the primitive map and integration map should NOT be aliases of each other. They should be deepcopies instead.

3. Map of temporary cell-centered values for tracking the total change in a quantity over a timestep.

   • This map holds key-array pairs named for all integration quantities. For each (partial) timestep, these arrays are used to accumulate the total change in the conserved form of each quantity. This includes the flux divergence and the contributions from source terms. At the end of the (partial) timestep, these are used to actually update the values of the integration quantities

4. Map of reconstructed left/right primitive quantites

   • 2 instances of EnzoEFltArrayMap are used to respectively hold the reconstructed left and right interface primitive quantities. This should share have the same keys that are described for the second category of maps.

   • These maps are frequently passed to instances of EnzoReconstructor to store the reconstructed passively advected scalars and primitive quantities. Then, these are frequently passed to EnzoRiemann to compute fluxes for the integration quantities and passively advected scalars.

5. Maps of Riemann Flux fields

   • An instance of this kind of map is required for each dimension and is used to hold the face-centered fluxes along that dimension. The contained arrays should all be defined with the appropriate shape for holding data stored on the mesh face along the dimension corresponding to the flux. In other words, if a block normally holds n elements (including ghost zones) along axis i, then an array used to store fluxes along axis i should hold n-1 elements along axis i.

   • This should have all of the same keys that are in the the first category of maps.

   • This kind of map should contain keys named for all passively advected scalars and registered integration quantities. The set of keys in these maps should be identical to the set of keys in the first category of maps, regardless of whether a quantity is “specific” or “conserved” (e.g. the map will hold a “velocity_x” key even though the associated array stores the x-component of the momentum density flux).

In general, the use of EnzoEFltArrayMap objects with common sets of keys helps simplify the implementation of various methods (e.g. the cell-centered array associated with “density” is used to reconstruct values that are stored in the fields of the “density” array in the primitive map).

Equation Of State

All of the operations related to the equation of state are handled by subclasses of the abstract base class, EnzoEquationOfState. The class has a number of responsibilities. Currently the only concrete subclass of EnzoEquationOfState is the EnzoEOSIdeal class which encapsulates the properties of an ideal, adiabatic gas. This class can optionally support use of the dual-energy formalism (For details about the currently expected implementation of the dual-energy formalism see the "modern" section of dual-energy formalism ).

The EnzoEquationOfState has the following interface:

bool is_barotropic();

Returns whether the equation of state is barotropic or not.

Currently, no barotropic equations of state have been implemented and none of the wavespeed calculations for the Riemann solvers currently support barotropic equations of state.

bool uses_dual_energy_formalism();

Returns whether the dual energy formalism is in use.

enzo_float get_gamma();

Returns the ratio of the specific heats. This is only required to yield a reasonable value if the gas is not barotropic.

enzo_float get_isothermal_sound_speed();

Returns the isothermal sound speed. This is only required to yield a reasonable value for barotropic equations of state.

enzo_float get_density_floor();

Returns the density floor.

enzo_float get_pressure_floor();

Returns the thermal pressure floor.

apply_floor_to_energy_and_sync(EnzoEFltArrayMap &integration_map,
                               int stale_depth);

This method applies the applies the pressure floor to the total_energy array specified in integration_map. If using the dual-energy formalism the floor is also applied to the internal energy (also specified in integration_map) and synchronizes the internal energy with the total energy. If the equation of state is barotropic, this should do nothing.

void pressure_from_integration(const EnzoEFltArrayMap &integration_map,
                               const CelloArray<enzo_float, 3> &pressure,
                               int stale_depth,
                               bool ignore_grackle = false);

This method computes the pressure from the integration quantities (stored in integration_map) and stores the result in pressure. This wraps the EnzoComputePressure object whose default behavior is to use the Grackle-supplied routine for computing pressure when the simulation is configured to use EnzoMethodGrackle. The ignore_grackle parameter can be used to avoid using that routine (the parameter is meaningless if the Grackle routine would not otherwise get used). This parameter’s primary purpose is to provide the option to suppress the effects of molecular hydrogen on the adiabatic index (when Grackle is configured with primordial_chemistry > 1).

void primitive_from_integration
  (const EnzoEFltArrayMap &integration_map, EnzoEFltArrayMap &primitive_map,
   int stale_depth, const std::vector<std::string> &passive_list,
   bool ignore_grackle = false);

This method is responsible for computing the primitive quantities (to be held in primitive_map) from the integration quantities (stored in integration_map). Non-passive scalar quantities appearing in both integration_map and primitive_map are simply deepcopied and passive scalar quantities are converted from conserved-form to specific form. For a non-barotropic EOS, this also computes pressure (by calling EnzoEquationOfState::pressure_from_integration).

In the future, it might be worth considering making this into a subclass of Cello’s ``Physics`` class. If that is done, it may be advisable to allow for switching between different dual-energy formalism implementations.

How to extend

New equations of state can be added by subclassing and providing the subclass with implementations for the pure virtual functions EnzoEquationOfState. Once a second concrete subclass of EnzoEquationOfState is provided, it may be worthwhile to introduce a factory method.

Reconstructor

The reconstruction algorithms have been factored out to their own classes. All implementation of reconstruction algorithms are derived from the EnzoReconstructor abstract base class.

To get a pointer to an instance of a concrete implementation of EnzoReconstructor, use the EnzoReconstructor::construct_reconstructor static factory method:

EnzoReconstructor* construct_reconstructor
 (const std::vector<std::string> active_primitive_keys,
  std::string name, enzo_float theta_limiter);

The factory method requires that we register the keys of the non-passive scalar primitive quantities that are are to be reconstructed via active_primitive_keys. We specify the name of the reconstruction algorithm, name. Note that the primitive keys should correspond to quantities specified in FIELD_TABLE ; for more details about FIELD_TABLE, see Centered Field Registry

Public Interface

The main interface function provided by this class is:

void reconstruct_interface
  (const EnzoEFltArrayMap &prim_map, EnzoEFltArrayMap &priml_map,
   EnzoEFltArrayMap &primr_map, int dim, EnzoEquationOfState *eos,
   int stale_depth, const std::vector<std::string>& passive_list);

This function takes the cell-centered primtive quantities (specified by the contents of prim_map) and computes the left and right reconstructed states (the results are stored in priml_map and primr_map) along the dimension specifed by dim. If dim has a value of 0/ 1/ 2 then the values are reconstructed along the x-/y-/z-axis. stale_depth indicates the current stale_depth for the supplied cell-centered quantities (prior to reconstruction). priml_map and primr_map should have the same shapes as prim_map, except along the reconstruction axis; along that axis prim_map should be able to hold 1 more value. passive_list is used to specify the names (keys) of the passively advected quantities that are to be reconstructed.

The int EnzoReconstructor::immediate_staling_rate() method is provided to determine the amount by which the stale depth increases immediately after reconstruction, for a given algorithm. The int EnzoReconstructor::delayed_staling_rate() method returns how much the stale depth increases after adding flux divergence, computed from the reconstructed values, to the integration quantities (this is normally 1). Finally int EnzoReconstructor::total_staling_rate() gives the sum of the results yielded by the prior 2 methods.

How to extend

To add a new reconstructor, subclass EnzoReconstructor and provide definitions for the virtual methods. The implementations of the immediate_staling_rate() and total_staling_rate() virtual methods must also be provided. Additionally, the factory method EnzoReconstructor::construct_reconstructor must also be modified to return pointers to instances of the new class when the appropriate name is passed as an argument, and the name of the new reconstructor should be added to reconstruction

Currently, to add new slope limiters for existing reconstruction algorithms new classes are effectively defined. The piecewise linear reconstruction algorithm is implemented as a class template EnzoReconstructorPLM<Limiter> where Limiter is a functor that implements a specific slope limiter. Limiter must be default constructible and provide a function call operation, operator(). The function call operation must have a signature matching:

enzo_float Functor::operator()(enzo_float vm1, enzo_float v, enzo_float vp1,
                               enzo_float theta_limiter);

Give three contiguous primitive values along the axis of interpolation, (vm1, v, and vp1) the method should compute the limited slope. The theta_limiter parameter that can be optionally used to tune the limiter (or ignored).

When a new a Limiter functor is defined to be used to specialize EnzoReconstructorPLM, the new specialization must be added to enzo.CI. The other steps mentioned at the start of this subsection for implementing new reconstruction algorithms must also be followed.

The use an enum with a switch statement was considered for switching between different slope limiters. However we determined that the compiler would not pull the switch statement outside of the loop. Therefore templates are used to avoid executing the switch statement on every single iteration.

Having multiple slope limiters available at runtime may be unnecessary (or not worth the larger binary size). It might be worth considering using preprocessor macros to allow for specification of the slope limiter at compile time.

Riemann Solver

All implementations of (approximate) Riemann solver algorithms are derived from the EnzoRiemann abstract base class.

Usage Notes

To get a pointer to a concrete implemenation of EnzoRiemann, call the static factory method:

EnzoRiemann* EnzoRiemann::construct_riemann
(const EnzoRiemann::FactoryArgs& factory_args) noexcept;

The above signature looks a little intimidating. In reality, you could write something more like the following snippet

EnzoRiemann* ptr = EnzoRiemann::construct_riemann({solver, mhd,
                                                   internal_energy});

in which

• solver is a std::string specifying the name of the solver

• mhd is a boolean specifying whether magnetic fields are present

• internal_energy is a boolean specifying if the internal energy flux must be computed.

This weird indirection only currently exists to accomodate charm++'s pup functionality. Once Enzo-E transitions to its custom restart functionallity, we’ll remove this indirection.

An instance of EnzoRiemann specifies the expected non-passive keys (and key-order) that the flux_map argument should have when passed to its solve method (these keys correspond to integration quantities).

const std::vector<std::string> integration_quantity_keys() const;

The following method specifies the expected non-passive keys (and key-order) that the priml_map and primr_map arguments should have when passed an EnzoRiemann's solve method (these keys correspond to primitive quantities).

const std::vector<std::string> primitive_quantity_keys() const;

The main interface function of EnzoRiemann is:

void solve(const EnzoEFltArrayMap &prim_map_l,
           const EnzoEFltArrayMap &prim_map_r,
           EnzoEFltArrayMap &flux_map, int dim, EnzoEquationOfState *eos,
           int stale_depth, const str_vec_t &passive_list,
           const CelloArray<enzo_float,3> * const interface_velocity) const;

In this function, the prim_map_l and prim_map_r arguments are references to the EnzoEFltArrayMap objects holding the arrays of reconstructed left/right primitive quantities. The flux_map argument holds the face-centered arrays where the computed fluxes for each integration quantity are written. dim indicates the dimension along which the flux should be computed (0,1,2 corresponds to x,y,z). interface_velocity is an optional argument used to specify a pointer to an array that can be used to store interface velocity values computed by the Riemann Solver (this is primarily used for computing internal energy source terms when the dual energy formalism is in use).

Some additional notes:

• The first EnzoRiemann::primitive_quantity_keys().size() keys of prim_map_l and prim_map_r should match the values and order of EnzoRiemann::primitive_quantity_keys().

• Likewise, the first EnzoRiemann::integration_quantity_keys().size() keys of flux_map should match the values and order of EnzoRiemann::integration_quantity_keys().

• prim_map_l, prim_map_r, and flux_map should also each contain keys for each of the passive scalars in passive_list (the order of these is not currently enforced).

• All of the arrays in prim_map_l, prim_map_r, and flux_map should have the same shape. If interface_velocity is specified, it should also have that shape.

• Calling the contiguous_arrays() instance method for prim_map_l, prim_map_r, and flux_map must return true in each case (in other words, each array in the array maps should be stored in nearly-contiguous 4D arrays).

Implementation Notes: Kernels

At the time of writing, the calculations specific to each Riemann Solver are implemented as kernels (inspired by Kokkos). More precise requiements are detailed in Kernel Requirements, but in short each kernel:

• defines a operator()(int iz, int iy, int ix) const method for computing the flux at the specified cell-interface

• specifies a specialization of the template class EnzoRiemannLUT<InputLUT>. This both indicates the expected actively advected integration (and primitive) quantities AND acts as a compile-time lookup table (that maps quantity names to unique array indices). See EnzoRiemannLUT for more details.

• Specifies the expected equation of state, by specifying the expected type of EOS Struct objects. See EOSStruct Objects for more details about EOS Struct objects.

• are configured by an instance of KernelConfig<EOSStructT> (see KernelConfig<EOSStructT> for more details).

The EnzoRiemannImpl<Kernel> class template is used to wrap each kernel. This class template subclasses the EnzoRiemann abstract base class and is used to implement the interface described above, in Usage Notes, for each kernel (i.e. in other words, we use it to implement “type erasure”). In more detail, EnzoRiemannImpl<Kernel>::integration_quantity_keys() and EnzoRiemannImpl<Kernel>::primitive_quantity_keys() methods specify the fields (and field ordering) required by a given kernel.

The steps of EnzoRiemannImpl<Kernel>::solve are fairly straight-forward:

1. An instance of KernelConfig<Kernel::EOSStructT> is created.

2. The Kernel is constructed and executed at each cell-interface

3. The fluxes for passively advected scalars are computed (this step is completely independent of the choice of Kernel).

EnzoRiemannLUT

As described above in the Overview, we sought to avoid the common approach of hydro codes that map actively advected quantities indices with macros or globally defined unscoped enums. The EnzoRiemannLUT<InputLUT> template class basically serves as a compromise between this traditional approach approach and using a hash table (which introduce unacceptable overhead) for organizing quantities in the main loop of EnzoRiemannImpl<Kernel>. Alternatively it can be thought of as a scoped version of the traditional approach.

This is a template class that provides the following features at compile time:

• a lookup table (LUT) that maps the names of components of a subset of the actively advected integration quantities defined in FIELD_TABLE to unique, contiguous indices.

• the number of integration quantity components included in the table

• a way to iterate over just the conserved or specific integration quantities values that are stored in an array using these mapping

• a way to query which of the actively advected integration quantities in FIELD_TABLE are not included in the LUT

These feature are provided via the definition of publicly accessible integer constants in every specialization of the template class. All specializations have:

• a constant called num_entries equal to the number of integration quantity components included in the lookup table

• a constant called specific_start equal to the number of components of conserved integration quantities included in the lookup table

• qkey constants, which include constants named for the components of ALL actively advected integration quantities in FIELD_TABLE. A constant associated with a SCALAR quantity, {qname}, is simply called {qname} while constants associated with a vector quantity {qname} are called {qname}_i, {qname}_j, and {qname}_k.

The qkey constants serve as both the keys of the lookup table and a way to check whether a component of an actively advected quantity is included in the table. Their values are satisfy the following conditions:

• All constants named for values corresponding to quantities NOT included in the lookup table have values of -1

• All constants named for conserved integration quantities have unique integer values in the internal [0,specific_start)

• All constants named for specific integration quantities have unique integer values in the interval [specific_start, num_entries)

• Constants must be defined for all 3 components (or none of the components) of a vector quantity (e.g. velocity or magnetic fields). Additionally, the kth component of a vector quantity is expected to have a value that is 1 larger than that of the jth component and 2 larger than the ith component.

The lookup table is always expected to include density and the 3 velocity components.

This template class also provides a handful of helpful static methods to programmatically probe the table’s contents at runtime and validate that the above requirements are specified.

For the sake of providing some concrete examples about how the code works, let’s assume that we have a class MyIntegLUT that is defined as:

struct MyIntegLUT {
  enum vals { density=0, velocity_i, velocity_j, velocity_k,
              total_energy, num_entries, specific_start = 1};
};

The template specialization EnzoRiemannLUT<MyIntegLUT> assumes that all undefined qkey constants omitted from MyIntegLUT are not included in the lookup table and will define them within the template specialization to have values of -1.

To access the index associated with density or the jth component of velocity, one would evaluate:

int density_index = EnzoRiemannLUT<MyIntegLUT>::density; //=0
int vj_index = EnzoRiemannLUT<MyIntegLUT>::velocity_j;   //=2

Additionally, the value of EnzoRiemannLUT<MyIntegLUT>::bfield_k would be -1.

It makes more sense to talk about the use of this template class when we have a companion array. For convenience, the alias template lutarray<LUT> type is defined. The type, lutarray<EnzoRiemannLUT<InputLUT>> is an alias of the type std::array<enzo_float, EnzoRiemannLUT<InputLUT>::num_entries>;.

As an example, imagine that the total kinetic energy density needs to be computed at a single location from an values stored in an array, integ, of type lutarray<EnzoRiemannLUT<MyIntegLUT>>:

using LUT = EnzoRiemannLUT<MyIntegLUT>;
enzo_float v2 = (integ[LUT::velocity_i] * integ[LUT::velocity_i] +
                 integ[LUT::velocity_j] * integ[LUT::velocity_j] +
                 integ[LUT::velocity_k] * integ[LUT::velocity_k]);
enzo_float kinetic = 0.5 * integ[LUT::density] * v2;

EnzoRiemannLUT<InputLUT>, makes it very easy to write generic code that can be reused for multiple different lookup table by using by passing its concrete specializations as a template argument to other template functions/classes. Consider the case where a single template function is desired to compute the total non-thermal energy density at a single location for an arbitrary lookup table:

template <class LUT>
enzo_float calc_nonthermal_edens(lutarray<LUT> prim)
{
  enzo_float v2 = (prim[LUT::velocity_i] * prim[LUT::velocity_i] +
  prim[LUT::velocity_j] * prim[LUT::velocity_j] +
  prim[LUT::velocity_k] * prim[LUT::velocity_k]);

  enzo_float bi = (LUT::bfield_i >= 0) ? prim[LUT::bfield_i] : 0;
  enzo_float bj = (LUT::bfield_j >= 0) ? prim[LUT::bfield_j] : 0;
  enzo_float bk = (LUT::bfield_k >= 0) ? prim[LUT::bfield_k] : 0;
  enzo_float b2 = bi*bi + bj*bj + bk*bk;

  return 0.5(v2*prim[LUT::density] + b2);
}

EOSStruct Objects

These objects are supposed to be lightweight struct/classes that encapsulate an equation of state. It’s also important that these objects are cheap to copy. It’s our intention to keep these independent of the other Riemann Solver tooling (particularly EnzoRiemannLUT).

Our only concrete example at this time is EOSStructIdeal. But this very much expresses the basic idea. The struct provides methods that just require density and pressure values to compute:

• specific internal energy

• internal energy density

• sound speed

• fast magnetosonic speed (this requires magnetic field values to also be specified)

In the future, we may need to slightly revisit the expected signature if/when we add support for an isothermal fluid.

Note

At this time, EOSStructIdeal is completely independent of the EnzoEOSIdeal subclass of EnzoEquationOfState.

In the immediate future, there are plans to unify these implementations (the EnzoEquationOfState machinery will be refactored to make use of these EOSStruct objects). When that comes to pass, we will flesh out this section in greater detail.

KernelConfig<EOSStructT>

The KernelConfig template class simply groups the configuration parameters for kernel (the alternative would be to require that the members of KernelConfig are listed as members for every class implementing a kernel).

The relationship between this class and a kernel is modelled after the relationship between captured values and a lambda function. We made this class as lightweight as possible to encourage the compiler to make similar optimizations. The declaration of KernelConfig is reproduced below:

template<typename EOSStructT>
struct KernelConfig{
  /// @class    KernelConfig
  /// @ingroup  Enzo
  /// @brief    [\ref Enzo] Stores the configuration options, input arrays, and
  /// output arrays used by a Riemann Solver Kernel.
  ///
  /// To help facilitate optimizations, we avoid introducing methods and
  /// declare all member variables to be ``const``
  ///
  /// Indices passed to the trailing 3 axes of ANY array (3D & 4D) held by this
  /// struct are used to specify spatial position of values.
  /// - In practice, it's sufficient to understand that a given set of spatial
  ///   indices, `(iz,iy,ix)`, represent the same spatial location in each array
  /// - For completeness, we note that integer indices map to the center of the
  ///   x-faces, y-faces, & z-faces for `dim` values of 0, 1, & 2, respectively.
  ///   The extents of these trailing spatial axes `(LENz, LENy, LENx)` are:
  ///   - when `dim=0`: `LENz = mz`,     `LENy = my`,     `LENx = mx-1`
  ///   - when `dim=1`: `LENz = mz`,     `LENy = my - 1`, `LENx = mx`
  ///   - when `dim=2`: `LENz = mz - 1`, `LENy = my`,     `LENx = mx`
  ///   where `(mz,my,mx)` gives the number of cells along each axis of a
  ///   cell-centered field (including the ghost zone)

  /// @name ConfigOptions
  /**@{*/
  /// dimension along which the flux is being computed (0 -> x, 1 -> y, 2 -> z)
  const int dim;
  /// EOS Struct Object
  const EOSStructT eos;
  /**@}*/

  /// @name PrimaryArrays
  /// `prim_arr_l` and `prim_arr_r` provide a kernel's primary input data. The
  /// primary outputs get written to `flux_arr`. All 3 arrays share the shape:
  /// `(LUT::num_entries, LENz, LENy, LENx)`
  ///
  /// The index passed to axis 0 correspond to different quantities (a kernel's
  /// `LUT` specifies the precise mapping between quantities & index values).
  /// There are 2 relevant points to be mindful of:
  /// 1. for these arrays, when accessing components of vector quantities
  ///    (e.g. `LUT::velocity_i`, `LUT::velocity_j`, or `LUT::bfield_k`),
  ///    the i, j, & k components ALWAYS map to the x, y, and z components.
  /// 2. For performance purposes, the length of the arrays along axis 0 is
  ///    allowed to exceed `LUT::num_entries`. But kernels should never
  ///    access these indices (they don't map to quantities in LUT)
  /// For completeness, we provide the following examples:
  /// - `flux_arr(LUT::density,...)` & `flux_arr(LUT::velocity_k,...)`
  ///   are where the computed density & momentum_z fluxes should be stored
  /// - `prim_arr_l(LUT::density,...)` & `prim_arr_l(LUT::velocity_i,...)` hold
  ///   the reconstructed density & velocity_x values on the left side of a
  ///   cell interface
  /**@{*/
  /// array to store the computed fluxes
  const CelloArray<enzo_float,4> flux_arr;
  /// array of primitives reconstructed on the left side of cell interfaces
  const CelloArray<const enzo_float,4> prim_arr_l;
  /// array of primitives reconstructed on the right side of cell interfaces
  const CelloArray<const enzo_float,4> prim_arr_r;
  /**@}*/

  /// @name DualEnergyArrays
  /// These arrays store outputs used in the dual-energy formalism and have the
  /// shape `(LENz, LENy, LENx)`.
  ///
  /// For any Dual-Energy compatible EOS, kernels should ALWAYS fill these
  /// arrays with the relevant values. If the dual energy formalism isn't used
  /// outside of the Riemann Solver, these are initialized with scratch-space.
  /// This is done to avoid unnecessary branching and code generation.
  /**@{*/
  /// array to store the computed flux for the specific internal energy
  ///
  /// @note
  /// When `flux_arr.shape(0) > LUT::num_entries`, this can technically alias
  /// one of `flux_arr`'s subarrays without a corresponding `LUT` entry. In
  /// practice, kernels will NEVER be affected by this.
  const CelloArray<enzo_float,3> internal_energy_flux_arr;
  /// array to store the velocity (along `dim`) computed at the cell interface
  const CelloArray<enzo_float,3> velocity_i_bar_arr;
  /**@}*/
};

Note

In the near-future, the above snippet will be replaced with nicer looking documentation that will be auto-generated using doxygen and breathe

More details will be given below about internal energy calculations.

Kernel Requirements

The basic skeleton for defining a kernel is defined below. For concreteness, we’ve assumed that this kernel uses the MHDLUT and an ideal EOS (but those could easily be changed).

struct MyKernel
{

public: // typedefs
  using LUT = EnzoRiemannLUT<MHDLUT>;
  using EOSStructT = EOSStructIdeal;

public: // fields
  const KernelConfig<EOSStructT> config;

public: // methods
  FORCE_INLINE void operator()(const int iz,
                               const int iy,
                               const int ix) const noexcept
  {
    // compute the fluxes at (iz, iy, ix) & store result in config.flux_arr
    //
    // For concreteness:
    //   - the left and right reconstructed density values (for the same
    //     cell-interface) can be retrieved using:
    //       config.prim_arr_l(LUT::density, iz, iy, ix)
    //       config.prim_arr_r(LUT::density, iz, iy, ix)
    //   - we want to write computed density flux to:
    //       config.flux_arr(LUT::density, iz, iy, ix)
    //
    // It may be helpful to point out that:
    //   when (config.dim == 0) -> this should computes on x-faces
    //   when (config.dim == 1) -> this should computes on y-faces
    //   when (config.dim == 2) -> this should computes on z-faces
    //
    // For more information, including how exactly indices map to spatial
    // locations, check the docstrings for KernelConfig. In practice, it's
    // sufficient to understand that (iz,iy,ix) refers to the same spatial
    // location in ALL of the arrays.
    //
    // assuming it makes sense for the EOS (it's non-barotropic), this should
    // also compute values needed for the dual energy formalism and store
    // results in config.internal_energy_flux_arr(iz,iy,ix) &
    // config.velocity_i_bar_arr(iz,iy,ix)

  }
};

There are a couple of things to note:

• As explained in KernelConfig<EOSStructT>, when you access vector quantities from config.prim_arr_l, config.prim_arr_r, or config.flux_arr using LUT (e.g. LUT::velocity_i, LUT::velocity_j, LUT::bfield_k), the i, j, & k components always map to the x, y, & z components, respectively.

  • To be concrete: config.flux_arr(LUT::velocity_j, iz, iy, ix) always refers to the flux of the y velocity component.

  • To try preserve symmetry, we often use config.dim to remap the i, j, and k components (like what is done in Athena++). The current convention is to include the following code block at the start of operator():

    const int external_velocity_i = config.dim + LUT::velocity_i;
    const int external_velocity_j = ((config.dim+1)%3) + LUT::velocity_i;
    const int external_velocity_k = ((config.dim+2)%3) + LUT::velocity_i;
    const int external_bfield_i = config.dim + LUT::bfield_i;
    const int external_bfield_j = ((config.dim+1)%3) + LUT::bfield_i;
    const int external_bfield_k = ((config.dim+2)%3) + LUT::bfield_i;
    

    and to use external_velocity_i, external_velocity_j, external_velocity_k instead of LUT::velocity_i, LUT::velocity_j, LUT::velocity_k when accessing values from prim_arr_l, prim_arr_r, and flux_arr.

  • We have given some thought to trying to abstract this vector permutation, but it unfortunately remains unclear how to do this in a way that preserves performance across different compilers, without requiring template specializations of operator() for computing fluxes along different dimensions.

• It’s also possible to make config a private field or to introduce additional fields. However, if you do either of those things, you will need to define a constructor that accepts config as a single argument.

• FORCE_INLINE is a macro that uses compiler-specific extensions to force inlining of functions. Please use this sparingly outside, only in cases where you see a noticable speedup (inlining everything can actually slow code down from inflating the binary’s size).

Dual Energy Formalism Treatment

The dual-energy formalism requires that a Riemann Solver computes fluxes for the internal energy, and a velocity component at the cell-interfaces.

Computing these quantities doesn’t change the Riemann Solver calculation (or the required reconstructed primitives), it just involves an extra calculation. To avoid unnecessary template code generation or introducing branching:

• EnzoRiemannLUT generally does not include internal_energy as an entry (there are other reasons why this is convenient)

• Kernels always compute the necessary quantities for the dual-energy formalism (assuming the EOS is compatible with the dual-energy formalism)

Instead, EnzoRiemannImpl<Kernel> manages the dual-energy configuration:

• EnzoRiemannImpl<Kernel>::solve will ALWAYS make sure that config.internal_energy_flux_arr and config.velocity_i_bar_arr are valid arrays. If arrays aren’t provided (i.e. the dual-energy formalism is not in use), scratch data will be used for this explicit purpose.

• EnzoRiemannImpl<Kernel> is responsible for including "internal_energy" in the output of integration_quantity_keys(), based on how it’s configured.

Adding new quantites

To add support for new actively advected integration cell-centered quantities (e.g. cosmic ray energy/flux), the table of cell-centered quantities (FIELD_TABLE) must be updated. See Centered Field Registry for more details. To add support for computing fluxes for such quantities, modifications must be made to either EnzoRiemannImpl or the Kernel of an existing solver. Alternatively, for certain quantities, a brand new solver may need to be introduced.

When adding a new integration vector quantity, you also need to add a few lines to the main for-loop of EnzoRiemannImpl for copying values to wl/wr and from fluxes (The existing code doing this for the velocity and magnetic fields should be used as a guide).

Adding new solvers

New Riemann Solvers can currently be added to the infrastructure by either subclassing EnzoRiemann or defining a new specialization of EnzoRiemannImpl<Kernel>. In either case, the EnzoRiemann::construct_riemann factory method must be modified to return the new solver and riemann solvers should be updated.

The additional steps for implementing a new Riemann solver by speciallizing EnzoRiemannImpl<Kernel> are as follows:

1. Define a new Kernel class (e.g. HLLDKernel)

2. (optional) define an alias name for the specialization of EnzoRiemannImpl that uses the new Kernel class (e.g. using EnzoRiemannHLLD = EnzoRiemannImpl<HLLDKernel>;).

Note

Due to the template-heavy nature of our implementation, the Riemann Solvers been separated from the rest of the Enzo-layer into their own sub-library.

This choice was made because the convention in the Enzo-layer (at least before we made this separation) is to effectively include every header file in every source file. Since template code usually needs to be written in header files, changes to the Riemann Solver algorithms used to frequently trigger rebuilds of the entire Enzo-layer. This separation has significantly sped up incremental rebuilds during the development workflow for the Riemann Solvers.

Updating integration quantities

The EnzoIntegrationQuanUpdate class has been provided to encapsulate the operation of updating integration quantities after a (partial) time-step. The operation was factored out of the EnzoMethodMHDVlct class since it appear in all Godunov solvers.

The constructor for EnzoIntegrationQuanUpdate has the following signature:

EnzoIntegrationQuanUpdate(std::vector<std::string> integration_quantity_keys,
                          bool skip_B_update)

The function requires that we:

• register the keys of the integration quantities (with integration_quantity_keys)

• indicate whether the update to the magnetic field should be skipped.

The integration quantity keys should match the names specified in FIELD_TABLE; see Centered Field Registry for more details. The update to the magnetic field should be skipped when Constrained Transport is in use (since the magnetic field update is handled separately). If the magnetic field is not specified as an integration quantity, then the value specified for skip_B_update is unimportant

The following method is used to compute the change in (the conserved form of) the integration and passively advected quantites due to the flux divergence along dimension dim over the (partial) timestep dt. The arrays in dUcons_map are used to accumulate the total changes in these quantities. passive_list lists the names (keys) of the passively advected scalars.

void accumulate_flux_component
  (int dim, double dt, enzo_float cell_width,
  const EnzoEFltArrayMap &flux_map,
   EnzoEFltArrayMap &dUcons_map, int stale_depth,
   const std::vector<std::string> &passive_list) const;

The method used to clear the values of the arrays used for accumulation is provided below. This sanitization should be performed before starting to accumulate flux divergence or source terms. The passive_list argument is used in the same way as the previous function.

void clear_dUcons_group(EnzoEFltArrayMap &dUcons_map, enzo_float value,
                        const std::vector<std::string> &passive_list) const;

The method used to actually add the accumulated change in the integration (specified in dUcons_map) to the values of the integration quantities from the start of the timestep (specificed by initial_integration_map) has the following signature:

void update_quantities
  (EnzoEFltArrayMap &initial_integration_map,
   const EnzoEFltArrayMap &dUcons_map,
   EnzoEFltArrayMap &out_integration_map,
   EnzoEFltArrayMap &out_conserved_passive_scalar,
   EnzoEquationOfState *eos, int stale_depth,
   const std::vector<std::string> &passive_list) const;

The fields included in dUcons_map should include contributions from both the flux divergence AND source terms. The results for the actively advected quanties are stored in out_integration_map and the results for the passively advected scalars are stored in conserved form in the arrays held by out_conserved_passive_scalar (note that the initial values of the passive scalars specified in initial_integration_map are in specific form).

Magnetic Field Integration

Subclasses of the abstract base class, EnzoBfieldMethod are used to implement magnetic field integration-related operations. While operations like reconstruction and flux calculations of relevant quantities are expected to be carried out with EnzoReconstructor and EnzoRiemann, all other magnetic field integration-related operations should be encapsulated by EnzoBfieldMethod.

Currently, the only subclass is EnzoBfieldMethodCT, which implements operations related to Constrained Transport. Other subclasses could be implemented in the future that encapsulate other integration methods (e.g. divergence cleaning).

From the perspective of an integrator that employs EnzoBfieldMethod, the primary result of each operation is to modify the values cell-centered/reconstructed quantities, since that’s all the integrator directly needs to know about. In reality, side effects performed by these operations can be equally as important. For example, EnzoBfieldMethodCT implicitly needs to update face-centered magnetic field values (given that the face-centered values serve as the primary representation, and the cell-centered values are derived directly from them).

To accomplish these goals, EnzoBfieldMethod, basically implements a state machine. It basically provides 3 classes of methods: (i) state machine-methods, (ii) physics methods, and (iii) descriptor methods.

State Machine Methods

When the EnzoBfieldMethod is first constructed, it has an uninitialized state. During construction the number of partial timesteps (num_partial_timesteps) involved per cycle must be specified.

At the beginning of an integration cycle (when an EnzoBfieldMethod object is unitialized), the cello Block that is going to be integrated block that must be specified using the following method.

void register_target_block(Block *block) noexcept;

This method will correctly set the internal state and will invoke the virtual register_target_block_ method, which is used by subclasses to preload relevant data from block and for the delayed initialization of scratch arrays (since the shapes may not be known at construction).

Once a target block has been registerred, the EnzoBfieldMethod object is now ready to perform integration-related operations for the first partial timestep (the physics methods can now be called). The following method is used to increment the partial timestep:

void increment_partial_timestep() noexcept;

The target block is unregistered once this method to has been called num_partial_timesteps times. Any calls to register_target_block while a block is still registered will currently cause an error.

There are couple of things to keep in mind:

• Any calls to physics methods or other state machine or other when no target block is registered are not allowed.

• It’s EXTREMELY important that increment_partial_timestep is always invoked num_partial_timesteps after a target block is registered and before there is chance for blocks to migrate between nodes. In other words, the a target block should always be registerred and unregistered during a single call to the cello Method object that represents the integrator.

Physics Methods

These methods are actually used to perform the relevant magnetic field integration operations. Each method is a pure virtual method that must be implemented by a subclass (even if the method immediately returns). These methods were all written and named based on the operations of Constrained Transport (CT). In the future, additional methods may need to be introduced to facillitate the implementation of other magnetic field integration schemes.

These methods are listed below with brief description. For more details, please see the docstring. The methods are expected to generally be called in the general order that they are listed. While this isn’t currently enforced, incorrect results may arise if they aren’t called in the proper order.

In the context of CT, the following method is used to overwrite the reconstructed value magnetic field component that corresponds to the axis of reconstruction with the (internally tracked) face-centered value.

void correct_reconstructed_bfield(EnzoEFltArrayMap &l_map,
                                  EnzoEFltArrayMap &r_map, int dim,
                                  int stale_depth) noexcept;

The following method is used by EnzoBfieldMethodCT to take note of the upwind direction after computing the Riemann Fluxes along a dimension dim.

void identify_upwind(const EnzoEFltArrayMap &flux_map, int dim,
                     int stale_depth) noexcept;

Finally, the following method is used to actually update the cell-centered magnetic field values.

void update_all_bfield_components
  (EnzoEFltArrayMap &cur_prim_map, const EnzoEFltArrayMap &xflux_map,
   const EnzoEFltArrayMap &yflux_map, const EnzoEFltArrayMap &zflux_map,
   EnzoEFltArrayMap &out_centered_bfield_map, enzo_float dt,
   int stale_depth) noexcept;

In EnzoBfieldMethodCT this will also update the face-centered magnetic field values (it assumes that identify_upwind was called once for each dimension and uses the stored data). When using this alongside EnzoIntegrationQuanUpdate, care needs to be taken about the order in which this method is called relative to EnzoIntegrationQuanUpdate::update_quantities that accounts for the time when floors are applied to the total energy.

Descriptor Methods

These are virtual methods that can be invoked at any time after the EnzoBfieldMethod object has been constructed. These are used to describe requirements of the given magnetic field integration method.

Currently, only one such method exists:

void check_required_fields() const noexcept;

These may change in the future.

How to extend

Implementing a new method for magnetic field integration is fairly straight-forward. Basically all you have to do is implement a subclass of EnzoBfieldMethod. In addition to providing implementations for each each physics and descriptor method, the subclass also needs to implement:

void register_target_block_(Block *target_block,
                            bool first_initialization) noexcept;

As mentioned earlier, this method is called by register_target_block while registering a new target block. In this call the subclass should preload any data it will need from the target_block. The first_initialization argument indicate whether this is the first time a target_block is being registered after the instance has been constructed (this includes the first time following deserialization after a restart). It can be used to help with lazy intialization of scratch space.

Once a second concrete subclass of EnzoBfieldMethod is provided, it may be worthwhile to introduce a factory method.