Amr Class

The Amr class is designed to manage parts of the computation which do not belong on a single level, like establishing and updating the hierarchy of levels, global timestepping, and managing the different AmrLevels. Most likely you will not need to derive any classes from Amr. Our mature application codes use this base class without any derived classes.

One of the most important data members is an array of AmrLevels - the Amr class calls many functions from the AmrLevel class to do things like advance the solution on a level, compute a time step to be used for a level, etc.

AmrLevel Class

Pure virtual functions include:

computeInitialDt Compute an array of time steps for each level of refinement. Called at the beginning of the simulation.

computeNewDt Compute an array of time steps for each level of refinement. Called at the end of a coarse level advance.

advance Advance the grids at a level.

post_timestep Work after at time step at a given level. In this tutorial we do the AMR synchronization here.

post_regrid Work after regridding. In this tutorial we redistribute particles.

post_init Work after initialization. In this tutorial we perform AMR synchronization.

initData Initialize the data on a given level at the beginning of the simulation.

init There are two versions of this function used to initialize data on a level during regridding. One version is specifically for the case where the level did not previously exist (a newly created refined level).

errorEst Perform the tagging at a level for refinement.

StateData

The most important data managed by the AmrLevel is an array of StateData, which holds the scalar fields, etc., in the boxes that together make up the level.

StateData is a class that essentially holds a pair of MultiFabs: one at the old time and one at the new time. AMReX knows how to interpolate in time between these states to get data at any intermediate point in time. The main data that we care about in our applications codes (such as the fluid state) will be stored as StateData. Essentially, data is made StateData if we need it to be stored in checkpoints/plotfiles, and/or we want it to be automatically interpolated when we refine. An AmrLevel stores an array of StateData (in a C++ array called state). We index this array using integer keys (defined via an enum in, e.g., AmrLevelAdv.H):

enum StateType { Phi_Type = 0,
                 NUM_STATE_TYPE };

In our tutorial code, we use the function AmrLevelAdv::variableSetUp to tell our simulation about the StateData (e.g., how many variables, ghost cells, nodality, etc.). Note that if you have more than one StateType, each of the different StateData carried in the state array can have different numbers of components, ghost cells, boundary conditions, etc. This is the main reason we separate all this data into separate StateData objects collected together in an indexable array.

LevelBld Class

The LevelBld class is a pure virtual class for defining variable types and attributes. To more easily understand its usage, refer to the derived class, LevelBldAdv in the tutorial. The variableSetUp and variableCleanUp are implemented, and in this tutorial call routines in the AmrLevelAdv class, e.g.,

void
AmrLevelAdv::variableSetUp ()
{
    BL_ASSERT(desc_lst.size() == 0);

    // Get options, set phys_bc
    read_params();

    desc_lst.addDescriptor(Phi_Type,IndexType::TheCellType(),
                           StateDescriptor::Point,0,NUM_STATE,
                           &cell_cons_interp);

    int lo_bc[BL_SPACEDIM];
    int hi_bc[BL_SPACEDIM];
    for (int i = 0; i < BL_SPACEDIM; ++i) {
        lo_bc[i] = hi_bc[i] = amrex::BCType::int_dir;   // periodic boundaries
    }

    BCRec bc(lo_bc, hi_bc);

    StateDescriptor::BndryFunc bndryfunc(nullfill);
    bndryfunc.setRunOnGPU(true);  // I promise the bc function will launch gpu kernels.

    desc_lst.setComponent(Phi_Type, 0, "phi", bc,
                          bndryfunc);
}

We see how to define the StateType, including nodality, whether or not we want the variable to represent a point in time or an interval over time (useful for returning the time associated with data), the number of ghost cells, number of components, and the interlevel interpolation (See AMReX_Interpolator for various interpolation types). We also see how to specify physical boundary functions by providing a function (in this case, nullfill since we are not using physical boundary conditions), where nullfill is defined in Src/bc_nullfill.cpp in the tutorial source code.

Example: Advection_AmrLevel

The Advection_AmrLevel example is documented in detail here in the AMReX tutorial documentation.

The Src subdirectory contains source code that is specific to this example. Most notably is the AmrLevelAdv class, which is derived from the base AmrLevel class, and the LevelBldAdv class, derived from the base LevelBld class as described above. The subdirectory Src/Src_K contain GPU kernels.

The Exec subdirectory contains two examples: SingleVortex and UniformVelocity. Each subdirectory contains problem-specific source code used for initialization using a Fortran subroutine (Prob.f90) and specifying the velocity fields used in this simulation (face_velocity_2d_K.H and face_velocity_3d_K.H for the 2-D and 3-D problem, respectively). Build the code here by editing the GNUmakefile and running make.

The pseudocode for the main program is given below.

/* Advection_AmrLevel Pseudocode */
main()
  Amr amr;
  amr.init()
  loop {
    amr.coarseTimeStep()
      /* compute dt */
      timeStep()
        amr_level[level]->advance()
        /* call timeStep r times for next-finer level */
        amr_level[level]->post_timestep() // AMR synchronization
      postCoarseTimeStep()
      /* write plotfile and checkpoint */
  }
  /* write final plotfile and checkpoint */

Particles

There is an option to turn on passively advected particles. In the GNUmakefile, add the line USE_PARTICLES = TRUE and build the code (do a make realclean first). In the inputs file, add the line adv.do_tracers = 1. When you run the code, within each plotfile directory there will be a subdirectory called “Tracer”.

Copy the files from amrex/Tools/Py_util/amrex_particles_to_vtp into the run directory and type, e.g.,

python amrex_binary_particles_to_vtp.py plt00000 Tracer

To generate a vtp file you can open with ParaView (Refer to the chapter on Visualization).