AmrMesh

AmrMesh handles (almost) all spatial operations in chombo-discharge. Internally, AmrMesh contains a bunch of operators that are useful across classes, such as ghost cell interpolation operators, coarsening operators, and stencils for interpolation and extrapolation near the embedded boundaries. AmrMesh also contains routines for generation and load-balancing of grids based and also contains simple routines for allocation and deallocation of memory.

Note

AmrMesh only handles spatial operations, it otherwise has limited knowledge of numerical discretizations.

AmrMesh is an integral part of chombo-discharge, and users will never have the need to modify it unless they are implementing something entirely new. The behavior of AmrMesh is modified through its available input parameters.

Tip

AmrMesh C++ API

Main functionality

There are two main functionalities in AmrMesh:

  1. Building grid hierarchies, and providing geometric information

  2. Providing AMR operators.

The grids in AmrMesh consist of a DisjointBoxLayout (see Chombo-3 basics) on each level, supported also by the EB information (EBISLayout). Recall that each grid patch in a DisjointBoxLayout is owned by a unique rank. However, since chombo-discharge supports multiple decompositions, we support the use of multiple DisjointBoxLayout describing the same grid level. Although these DisjointBoxLayout consist of the same boxes, the patch-to-rank mapping can be different (see Realm). To fetch a grid on a particular level, one can call AmrMesh::getGrids(const std::string a_realm). E.g.

const std::string myRealm;
const int myLevel;

const DisjointBoxLayout& dbl = m_amr->getGrids("myRealm")[myLevel];

Likewise, to fetch the geometric (EB) information for a specified realm, phase, and level:

const std::string myRealm;
const int myLevel;
const phase::which_phase myPhase;

const EBISLayout& ebisl = m_amr->getEBISLayout(myRealm, myPhase)[myLevel];

In addition to the grids, the user can fetch AMR operators. These are, for example, coarsening operators, interpolation operators, ghost cell interpolators etc. To save some regrid time, we don’t always build every AMR operator that we might ever need, but have solvers register the ones that they specifically need. See Realm for details.

The API of AmrMesh is quite extensive, and it has functionality both for providing grid operators as well as:

  • Maintaining overview of grids and operators.

  • Allocating grid and particle data.

  • Interpolating to new grids.

  • Coarsening data.

  • Updating ghost cells.

  • Interpolating data to e.g. EB centroids.

The AmrMesh API is a good place to start for figuring out the AmrMesh functionality.

Particle intersection

Class options

The class options below control AmrMesh:

  • AmrMesh.lo_corner. Low corner of problem domain (e.g. 0 0 0)

  • AmrMesh.hi_corner. High corner of problem domain (e.g. 1 1 1).

  • AmrMesh.verbosity. Class verbosity. Leave to -1 unless you are debugging.

  • AmrMesh.coarsest_domain. Number of grid cells on coarsest domain

  • AmrMesh.max_amr_depth. Maximum number of refinement levels.

  • AmrMesh.max_sim_depth. Maximum simulation depth. Values \(< 0\) means that grids can be generated with depths up to AmrMesh.max_amr_depth.

  • AmrMesh.fill_ratio. Fill ratio for BR grid generation

  • AmrMesh.irreg_growth. Buffer region around irregular tagged cells.

  • AmrMesh.buffer_size. Buffer size for BR grid generation.

  • AmrMesh.grid_algorithm. Grid generation algorithm. Valid options are br or tiled. See Mesh generation for details.

  • AmrMesh.box_sorting. Box sorting algorithm. Valid options are std, morton, or shuffle.

  • AmrMesh.blocking_factor. Blocking factor.

  • AmrMesh.max_box_size. Maximum box size.

  • AmrMesh.max_ebis_box. Maximum box size during EB geometry generation.

  • AmrMesh.ref_rat. Refinement ratios.

  • AmrMesh.num_ghost. Number of ghost cells for mesh data.

  • AmrMesh.lsf_ghost. Number of ghost cells when allocating level-set function on the grid.

  • AmrMesh.eb_ghost. Number of ghost cells for EB moments.

  • AmrMesh.centroid_sten. Which centroid interpolation stencils to use. Valid options are pwl, linear, taylor, lsq. Only linear is guaranteed monotone.

  • AmrMesh.eb_sten. EB interpolation stencils.

  • AmrMesh.redist_radius. Redistribution radius.

  • AmrMesh.ghost_interp. Default ghost cell interpolation type. Valid options are pwl or quad.

  • AmrMesh.ebcf. Can be set to false if refinement boundaries do not cross the EB. Valid options are true and false.

Warning

chombo-discharge only supports uniform resolution (i.e., cubic grid cells). I.e. the user must specify consist domain sizes and resolutions.

Runtime options

The following options are runtime options for AmrMesh:

  • AmrMesh.verbosity.

  • AmrMesh.fill_ratio.

  • AmrMesh.irreg_growth.

  • AmrMesh.buffer_size.

  • AmrMesh.grid_algorithm.

  • AmrMesh.box_sorting.

  • AmrMesh.blocking_factor.

  • AmrMesh.max_box_size.

These options only affect the grid generation method and parameters, and are thus only effective after the next regrid.